Hmdb loader

Showing metabocard for YGM 5A (HMDB0035454)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 20:26:37 UTC
Update Date2022-03-07 02:54:31 UTC
HMDB IDHMDB0035454
Secondary Accession Numbers
  • HMDB35454
Metabolite Identification
Common NameYGM 5A
DescriptionYGM 5A belongs to the class of organic compounds known as anthocyanidin 3-o-6-p-coumaroyl glycosides. These are anthocyanidin 3-O-glycosides where the carbohydrate moiety is esterified at the C6 position with a p-coumaric acid. P-coumaric acid is an organic derivative of cinnamic acid, that carries a hydroxyl group at the 4-position of the benzene ring. YGM 5A has been detected, but not quantified in, root vegetables. This could make YGM 5A a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on YGM 5A.
Structure
Data?1563862722
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035454 (YGM 5A)


  Mrv0541 02241208532D          

 76 83  0  0  0  0            999 V2000
    0.7143   -2.0624    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0007   -2.4748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4291   -2.4748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1440   -2.0624    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1440   -1.2374    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8576   -2.4748    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8576   -3.2998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1440   -3.7122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4291   -3.2998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7142   -3.7122    0.0000 O   0  3  0  0  0  0  0  0  0  0  0  0
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    0.7143   -4.5372    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4278   -4.9496    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4278   -5.7746    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1428   -6.1870    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4278   -3.2998    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
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 23 24  1  0  0  0  0
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 73 76  1  0  0  0  0
 74 75  2  0  0  0  0
M  CHG  1  11   1
M  END
Download

3D MOL for HMDB0035454 (YGM 5A)

HMDB0035454
     RDKit          3D
YGM 5A
129136  0  0  0  0  0  0  0  0999 V2000
    3.8803   -0.9442    5.8124 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1511   -0.1937    4.8087 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4080    0.3588    3.6766 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4602   -0.4289    2.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7265    0.0461    1.2563 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7096   -0.7963    0.0615 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7622   -0.6467   -0.7674 O   0  0  0  0  0  3  0  0  0  0  0  0
    5.9103   -1.3279   -1.8592 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0273   -1.1121   -2.6731 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1988   -1.8200   -3.8311 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3213   -1.6240   -4.6768 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2752   -2.7423   -4.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1164   -2.9923   -3.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2591   -3.8767   -3.7538 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2201   -4.6832   -3.7204 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9855   -4.0590   -3.9768 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -4.7544   -4.6273 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2018   -5.6632   -3.7656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4263   -4.8601   -2.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5159   -5.4070   -5.9091 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4476   -6.1909   -6.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7844   -6.1603   -5.7750 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5661   -7.5495   -6.0599 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4126   -5.9956   -4.4515 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8166   -6.1633   -4.5453 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.0347    0.6879    3.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8611    1.5777    2.8936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7939    2.3934    3.5208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6114    3.2436    2.8459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5523    3.3397    1.4626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3909    4.2051    0.8102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6224    2.5298    0.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5368    2.6047   -0.5683 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8016    1.6713    1.5351 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0760   -3.5126    1.6695 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9337   -4.3962    1.0279 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4000   -2.3777    0.7907 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3198   -1.1118    0.8979 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5229   -0.5348   -0.3458 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6878    0.8313   -0.2853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106    1.5856   -0.3638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2810    2.6425    0.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4759    3.4248    0.8473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1181    4.0443   -0.2678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2251    4.8690   -0.0548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5676    4.9885    1.1781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9784    5.5660   -1.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6785    5.5051   -2.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4520    6.2302   -3.3132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4986    6.9990   -2.9185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2864    7.7367   -3.8111 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8133    7.0699   -1.5635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0423    6.3507   -0.6807 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9012    3.4797    0.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8034    3.6341    1.1572 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6499    2.9373   -1.0709 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9956    3.3792   -1.0801 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6807    1.4512   -1.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3542    1.1045   -2.5116 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9606    1.4005    1.1265 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9180    2.2141    2.2453 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6520    1.7301    3.4856 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  1   7   1
M  END
Download

3D SDF for HMDB0035454 (YGM 5A)


  Mrv0541 02241208532D          

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M  CHG  1  11   1
M  END
> <DATABASE_ID>
HMDB0035454

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=CC(=C1)C1=[O+]C2=C(C=C1OC1OC(COC(=O)\C=C\C3=CC=C(O)C(O)=C3)C(O)C(O)C1OC1OC(COC(=O)C3=CC=C(O)C=C3)C(O)C(O)C1O)C(OC1OC(CO)C(O)C(O)C1O)=CC(O)=C2

> <INCHI_IDENTIFIER>
InChI=1S/C50H52O26/c1-67-31-13-22(6-10-27(31)55)45-32(16-25-29(70-45)14-24(53)15-30(25)71-48-43(64)40(61)37(58)33(17-51)73-48)72-50-46(42(63)39(60)34(75-50)18-68-36(57)11-3-20-2-9-26(54)28(56)12-20)76-49-44(65)41(62)38(59)35(74-49)19-69-47(66)21-4-7-23(52)8-5-21/h2-16,33-35,37-44,46,48-51,58-65H,17-19H2,1H3,(H4-,52,53,54,55,56,57,66)/p+1

> <INCHI_KEY>
DYZALFMOLIKHGK-UHFFFAOYSA-O

> <FORMULA>
C50H53O26

> <MOLECULAR_WEIGHT>
1069.9402

> <EXACT_MASS>
1069.282506868

> <JCHEM_ACCEPTOR_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
102.99990637808938

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-({3,4,5-trihydroxy-6-[(4-hydroxybenzoyloxy)methyl]oxan-2-yl}oxy)oxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium

> <ALOGPS_LOGP>
2.24

> <JCHEM_LOGP>
1.2430999999999988

> <ALOGPS_LOGS>
-3.67

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
8.115508542850556

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.653995450960224

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6858604180656585

> <JCHEM_POLAR_SURFACE_AREA>
413.5700000000001

> <JCHEM_REFRACTIVITY>
260.62989999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
18

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.35e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-({3,4,5-trihydroxy-6-[(4-hydroxybenzoyloxy)methyl]oxan-2-yl}oxy)oxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035454 (YGM 5A)

HMDB0035454
     RDKit          3D
YGM 5A
129136  0  0  0  0  0  0  0  0999 V2000
    3.8803   -0.9442    5.8124 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1511   -0.1937    4.8087 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4080    0.3588    3.6766 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4602   -0.4289    2.5180 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7265    0.0461    1.2563 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7096   -0.7963    0.0615 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7622   -0.6467   -0.7674 O   0  0  0  0  0  3  0  0  0  0  0  0
    5.9103   -1.3279   -1.8592 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0273   -1.1121   -2.6731 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1988   -1.8200   -3.8311 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3213   -1.6240   -4.6768 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2752   -2.7423   -4.1928 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1164   -2.9923   -3.3854 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2591   -3.8767   -3.7538 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2201   -4.6832   -3.7204 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9855   -4.0590   -3.9768 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0389   -4.7544   -4.6273 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2018   -5.6632   -3.7656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4263   -4.8601   -2.8088 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5159   -5.4070   -5.9091 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4476   -6.1909   -6.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7844   -6.1603   -5.7750 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5661   -7.5495   -6.0599 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4126   -5.9956   -4.4515 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8166   -6.1633   -4.5453 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9490   -2.2499   -2.1879 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8582   -2.4380   -1.3887 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7037   -1.6727   -0.1889 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5652   -1.9356    0.4945 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7698   -1.4516    1.4458 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6690   -2.0300    2.6465 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7694   -2.9973    2.9355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3041   -2.5465    3.9247 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1857   -1.6385    3.3896 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2076   -0.9399    3.9320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4530   -1.0775    5.1640 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0523   -0.0312    3.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0347    0.6879    3.6795 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8611    1.5777    2.8936 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7939    2.3934    3.5208 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6114    3.2436    2.8459 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5523    3.3397    1.4626 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3909    4.2051    0.8102 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6224    2.5298    0.8160 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5368    2.6047   -0.5683 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8016    1.6713    1.5351 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0760   -3.5126    1.6695 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9337   -4.3962    1.0279 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4000   -2.3777    0.7907 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8028   -2.2463    0.9136 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3198   -1.1118    0.8979 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5229   -0.5348   -0.3458 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6878    0.8313   -0.2853 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5106    1.5856   -0.3638 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2810    2.6425    0.5052 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4759    3.4248    0.8473 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1181    4.0443   -0.2678 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2251    4.8690   -0.0548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5676    4.9885    1.1781 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9784    5.5660   -1.0527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6785    5.5051   -2.3883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4520    6.2302   -3.3132 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4986    6.9990   -2.9185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2864    7.7367   -3.8111 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8133    7.0699   -1.5635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0423    6.3507   -0.6807 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9012    3.4797    0.1051 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8034    3.6341    1.1572 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6499    2.9373   -1.0709 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9956    3.3792   -1.0801 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6807    1.4512   -1.1649 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3542    1.1045   -2.5116 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9606    1.4005    1.1265 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9180    2.2141    2.2453 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6520    1.7301    3.4856 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6021    2.5287    4.6293 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6363   -0.3799    6.7703 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6829   -1.7013    6.1334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9777   -1.6292    5.6692 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3130   -1.4932    2.6188 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7745   -0.3761   -2.4093 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2977   -0.9425   -5.4390 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3530   -3.3349   -5.0984 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0518   -5.0317   -2.6233 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2847   -3.9688   -5.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5966   -6.1500   -4.3866 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7656   -6.4991   -3.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5175   -5.3923   -1.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6391   -4.6029   -6.6625 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7059   -7.1677   -6.3378 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5093   -5.8759   -6.5982 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4274   -8.0009   -6.1985 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0832   -6.8178   -3.7958 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0033   -6.3822   -5.4902 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1033   -3.1304   -1.6378 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1131   -0.3697    1.6548 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2725   -3.8649    3.3812 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8780   -3.4263    4.3188 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1874   -2.0916    4.8314 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8276    0.0440    2.1082 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1912    0.5835    4.7364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8625    2.3401    4.6032 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3254    3.8717    3.3506 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0634    4.7708    1.3321 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0987    3.2086   -1.1231 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1092    1.0539    0.9927 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8045   -5.2985    1.3586 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2827   -2.8127   -0.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.0334   -0.3645    1.6445 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9570    1.0121    0.8119 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0339    2.1306    1.4825 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.5277    4.4908   -0.1394 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4097    4.3993    1.0505 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2185    3.3617   -2.0217 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5087    3.0163   -1.7964 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7098    1.0566   -0.9342 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6415    0.4475   -2.5677 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1799    1.8487    0.1761 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1004    3.2745    2.0978 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4023    2.0988    5.5139 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  1   7   1
M  END
Download

PDB for HMDB0035454 (YGM 5A)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  O   UNK     0       1.333  -3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -0.001  -4.620   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.333  -3.850   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.668  -4.620   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.002  -3.850   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -4.002  -2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0      -5.334  -4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -5.334  -6.160   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.002  -6.929   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.668  -6.160   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.333  -6.929   0.000  0.00  0.00           O+1
HETATM   12  C   UNK     0      -0.001  -6.160   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.333  -6.929   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.333  -8.469   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.665  -9.239   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.665 -10.779   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       4.000 -11.549   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -6.669  -6.929   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.665  -6.160   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.000  -6.929   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.000  -8.469   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0       5.334  -9.239   0.000  0.00  0.00           O+0
HETATM   23  C   UNK     0      -5.334  -1.540   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -5.334   0.000   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -6.669   0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -8.001   0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -8.001  -1.540   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -6.669  -2.310   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -6.669  -3.850   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      -9.336   0.770   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -6.669   2.310   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -8.001   3.080   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0       1.333  -2.310   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0      -0.001  -1.540   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -0.001   0.000   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.333   0.770   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       2.665   0.000   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       2.665  -1.540   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0       4.000  -2.310   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       4.000   0.770   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       1.333   2.310   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0      -1.333   0.770   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -1.333   2.310   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -2.668   3.080   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -2.668   4.620   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0      -4.002   2.310   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0      -4.002   5.389   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      -4.002   6.929   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -5.334   7.699   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      -5.334   9.239   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -4.002  10.009   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      -2.668   9.239   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      -2.668   7.699   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      -1.333  10.009   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      -4.002  11.549   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0       5.334  -1.540   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0       5.334   0.000   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0       6.666   0.770   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0       8.001   0.000   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       8.001  -1.540   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0       6.666  -2.310   0.000  0.00  0.00           C+0
HETATM   63  O   UNK     0       6.666  -3.850   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       9.336  -2.310   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       9.336   0.770   0.000  0.00  0.00           O+0
HETATM   66  C   UNK     0       6.666   2.310   0.000  0.00  0.00           C+0
HETATM   67  O   UNK     0       8.001   3.080   0.000  0.00  0.00           O+0
HETATM   68  C   UNK     0       8.001   4.620   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0       6.666   5.389   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0       9.336   5.389   0.000  0.00  0.00           O+0
HETATM   71  C   UNK     0       5.334   4.620   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0       4.000   5.389   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0       4.000   6.929   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0       5.334   7.699   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0       6.666   6.929   0.000  0.00  0.00           C+0
HETATM   76  O   UNK     0       2.665   7.699   0.000  0.00  0.00           O+0
CONECT    1    2   34                                                       
CONECT    2    1    3   12                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   10                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5   23                                                       
CONECT    7    5    8                                                       
CONECT    8    7    9   18                                                  
CONECT    9    8   10                                                       
CONECT   10    4    9   11                                                  
CONECT   11   10   12                                                       
CONECT   12    2   11   13                                                  
CONECT   13   12   14   19                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16   21                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18    8                                                            
CONECT   19   13   20                                                       
CONECT   20   19   21                                                       
CONECT   21   15   20   22                                                  
CONECT   22   21                                                            
CONECT   23    6   24   28                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26   32                                                  
CONECT   26   25   27   31                                                  
CONECT   27   26   28   30                                                  
CONECT   28   23   27   29                                                  
CONECT   29   28                                                            
CONECT   30   27                                                            
CONECT   31   26                                                            
CONECT   32   25   33                                                       
CONECT   33   32                                                            
CONECT   34    1   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35   37   43                                                  
CONECT   37   36   38   42                                                  
CONECT   38   37   39   41                                                  
CONECT   39   34   38   40                                                  
CONECT   40   39   57                                                       
CONECT   41   38                                                            
CONECT   42   37                                                            
CONECT   43   36   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   46   47                                                  
CONECT   46   45   48                                                       
CONECT   47   45                                                            
CONECT   48   46   49                                                       
CONECT   49   48   50   54                                                  
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53   56                                                  
CONECT   53   52   54   55                                                  
CONECT   54   49   53                                                       
CONECT   55   53                                                            
CONECT   56   52                                                            
CONECT   57   40   58   62                                                  
CONECT   58   57   59                                                       
CONECT   59   58   60   66                                                  
CONECT   60   59   61   65                                                  
CONECT   61   60   62   64                                                  
CONECT   62   57   61   63                                                  
CONECT   63   62                                                            
CONECT   64   61                                                            
CONECT   65   60                                                            
CONECT   66   59   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69   70                                                  
CONECT   69   68   71   75                                                  
CONECT   70   68                                                            
CONECT   71   69   72                                                       
CONECT   72   71   73                                                       
CONECT   73   72   74   76                                                  
CONECT   74   73   75                                                       
CONECT   75   69   74                                                       
CONECT   76   73                                                            
MASTER        0    0    0    0    0    0    0    0   76    0  166    0
END
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3D PDB for HMDB0035454 (YGM 5A)

COMPND    HMDB0035454
HETATM    1  C1  UNL     1       3.880  -0.944   5.812  1.00  0.00           C  
HETATM    2  O1  UNL     1       4.151  -0.194   4.809  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.408   0.359   3.677  1.00  0.00           C  
HETATM    4  C3  UNL     1       4.460  -0.429   2.518  1.00  0.00           C  
HETATM    5  C4  UNL     1       4.727   0.046   1.256  1.00  0.00           C  
HETATM    6  C5  UNL     1       4.710  -0.796   0.062  1.00  0.00           C  
HETATM    7  O2  UNL     1       5.762  -0.647  -0.767  1.00  0.00           O1+
HETATM    8  C6  UNL     1       5.910  -1.328  -1.859  1.00  0.00           C  
HETATM    9  C7  UNL     1       7.027  -1.112  -2.673  1.00  0.00           C  
HETATM   10  C8  UNL     1       7.199  -1.820  -3.831  1.00  0.00           C  
HETATM   11  O3  UNL     1       8.321  -1.624  -4.677  1.00  0.00           O  
HETATM   12  C9  UNL     1       6.275  -2.742  -4.193  1.00  0.00           C  
HETATM   13  C10 UNL     1       5.116  -2.992  -3.385  1.00  0.00           C  
HETATM   14  O4  UNL     1       4.259  -3.877  -3.754  1.00  0.00           O  
HETATM   15  C11 UNL     1       3.220  -4.683  -3.720  1.00  0.00           C  
HETATM   16  O5  UNL     1       1.986  -4.059  -3.977  1.00  0.00           O  
HETATM   17  C12 UNL     1       1.039  -4.754  -4.627  1.00  0.00           C  
HETATM   18  C13 UNL     1       0.202  -5.663  -3.766  1.00  0.00           C  
HETATM   19  O6  UNL     1      -0.426  -4.860  -2.809  1.00  0.00           O  
HETATM   20  C14 UNL     1       1.516  -5.407  -5.909  1.00  0.00           C  
HETATM   21  O7  UNL     1       0.448  -6.191  -6.359  1.00  0.00           O  
HETATM   22  C15 UNL     1       2.784  -6.160  -5.775  1.00  0.00           C  
HETATM   23  O8  UNL     1       2.566  -7.549  -6.060  1.00  0.00           O  
HETATM   24  C16 UNL     1       3.413  -5.996  -4.452  1.00  0.00           C  
HETATM   25  O9  UNL     1       4.817  -6.163  -4.545  1.00  0.00           O  
HETATM   26  C17 UNL     1       4.949  -2.250  -2.188  1.00  0.00           C  
HETATM   27  C18 UNL     1       3.858  -2.438  -1.389  1.00  0.00           C  
HETATM   28  C19 UNL     1       3.704  -1.673  -0.189  1.00  0.00           C  
HETATM   29  O10 UNL     1       2.565  -1.936   0.494  1.00  0.00           O  
HETATM   30  C20 UNL     1       1.770  -1.452   1.446  1.00  0.00           C  
HETATM   31  O11 UNL     1       1.669  -2.030   2.646  1.00  0.00           O  
HETATM   32  C21 UNL     1       0.769  -2.997   2.936  1.00  0.00           C  
HETATM   33  C22 UNL     1      -0.304  -2.546   3.925  1.00  0.00           C  
HETATM   34  O12 UNL     1      -1.186  -1.639   3.390  1.00  0.00           O  
HETATM   35  C23 UNL     1      -2.208  -0.940   3.932  1.00  0.00           C  
HETATM   36  O13 UNL     1      -2.453  -1.077   5.164  1.00  0.00           O  
HETATM   37  C24 UNL     1      -3.052  -0.031   3.170  1.00  0.00           C  
HETATM   38  C25 UNL     1      -4.035   0.688   3.679  1.00  0.00           C  
HETATM   39  C26 UNL     1      -4.861   1.578   2.894  1.00  0.00           C  
HETATM   40  C27 UNL     1      -5.794   2.393   3.521  1.00  0.00           C  
HETATM   41  C28 UNL     1      -6.611   3.244   2.846  1.00  0.00           C  
HETATM   42  C29 UNL     1      -6.552   3.340   1.463  1.00  0.00           C  
HETATM   43  O14 UNL     1      -7.391   4.205   0.810  1.00  0.00           O  
HETATM   44  C30 UNL     1      -5.622   2.530   0.816  1.00  0.00           C  
HETATM   45  O15 UNL     1      -5.537   2.605  -0.568  1.00  0.00           O  
HETATM   46  C31 UNL     1      -4.802   1.671   1.535  1.00  0.00           C  
HETATM   47  C32 UNL     1       0.076  -3.513   1.669  1.00  0.00           C  
HETATM   48  O16 UNL     1       0.934  -4.396   1.028  1.00  0.00           O  
HETATM   49  C33 UNL     1      -0.400  -2.378   0.791  1.00  0.00           C  
HETATM   50  O17 UNL     1      -1.803  -2.246   0.914  1.00  0.00           O  
HETATM   51  C34 UNL     1       0.320  -1.112   0.898  1.00  0.00           C  
HETATM   52  O18 UNL     1       0.523  -0.535  -0.346  1.00  0.00           O  
HETATM   53  C35 UNL     1       0.688   0.831  -0.285  1.00  0.00           C  
HETATM   54  O19 UNL     1      -0.511   1.586  -0.364  1.00  0.00           O  
HETATM   55  C36 UNL     1      -0.281   2.643   0.505  1.00  0.00           C  
HETATM   56  C37 UNL     1      -1.476   3.425   0.847  1.00  0.00           C  
HETATM   57  O20 UNL     1      -2.118   4.044  -0.268  1.00  0.00           O  
HETATM   58  C38 UNL     1      -3.225   4.869  -0.055  1.00  0.00           C  
HETATM   59  O21 UNL     1      -3.568   4.989   1.178  1.00  0.00           O  
HETATM   60  C39 UNL     1      -3.978   5.566  -1.053  1.00  0.00           C  
HETATM   61  C40 UNL     1      -3.678   5.505  -2.388  1.00  0.00           C  
HETATM   62  C41 UNL     1      -4.452   6.230  -3.313  1.00  0.00           C  
HETATM   63  C42 UNL     1      -5.499   6.999  -2.919  1.00  0.00           C  
HETATM   64  O22 UNL     1      -6.286   7.737  -3.811  1.00  0.00           O  
HETATM   65  C43 UNL     1      -5.813   7.070  -1.563  1.00  0.00           C  
HETATM   66  C44 UNL     1      -5.042   6.351  -0.681  1.00  0.00           C  
HETATM   67  C45 UNL     1       0.901   3.480   0.105  1.00  0.00           C  
HETATM   68  O23 UNL     1       1.803   3.634   1.157  1.00  0.00           O  
HETATM   69  C46 UNL     1       1.650   2.937  -1.071  1.00  0.00           C  
HETATM   70  O24 UNL     1       2.996   3.379  -1.080  1.00  0.00           O  
HETATM   71  C47 UNL     1       1.681   1.451  -1.165  1.00  0.00           C  
HETATM   72  O25 UNL     1       1.354   1.105  -2.512  1.00  0.00           O  
HETATM   73  C48 UNL     1       4.961   1.400   1.126  1.00  0.00           C  
HETATM   74  C49 UNL     1       4.918   2.214   2.245  1.00  0.00           C  
HETATM   75  C50 UNL     1       4.652   1.730   3.486  1.00  0.00           C  
HETATM   76  O26 UNL     1       4.602   2.529   4.629  1.00  0.00           O  
HETATM   77  H1  UNL     1       3.636  -0.380   6.770  1.00  0.00           H  
HETATM   78  H2  UNL     1       4.683  -1.701   6.133  1.00  0.00           H  
HETATM   79  H3  UNL     1       2.978  -1.629   5.669  1.00  0.00           H  
HETATM   80  H4  UNL     1       4.313  -1.493   2.619  1.00  0.00           H  
HETATM   81  H5  UNL     1       7.775  -0.376  -2.409  1.00  0.00           H  
HETATM   82  H6  UNL     1       8.298  -0.943  -5.439  1.00  0.00           H  
HETATM   83  H7  UNL     1       6.353  -3.335  -5.098  1.00  0.00           H  
HETATM   84  H8  UNL     1       3.052  -5.032  -2.623  1.00  0.00           H  
HETATM   85  H9  UNL     1       0.285  -3.969  -5.006  1.00  0.00           H  
HETATM   86  H10 UNL     1      -0.597  -6.150  -4.387  1.00  0.00           H  
HETATM   87  H11 UNL     1       0.766  -6.499  -3.302  1.00  0.00           H  
HETATM   88  H12 UNL     1      -0.517  -5.392  -1.956  1.00  0.00           H  
HETATM   89  H13 UNL     1       1.639  -4.603  -6.662  1.00  0.00           H  
HETATM   90  H14 UNL     1       0.706  -7.168  -6.338  1.00  0.00           H  
HETATM   91  H15 UNL     1       3.509  -5.876  -6.598  1.00  0.00           H  
HETATM   92  H16 UNL     1       3.427  -8.001  -6.198  1.00  0.00           H  
HETATM   93  H17 UNL     1       3.083  -6.818  -3.796  1.00  0.00           H  
HETATM   94  H18 UNL     1       5.003  -6.382  -5.490  1.00  0.00           H  
HETATM   95  H19 UNL     1       3.103  -3.130  -1.638  1.00  0.00           H  
HETATM   96  H20 UNL     1       2.113  -0.370   1.655  1.00  0.00           H  
HETATM   97  H21 UNL     1       1.272  -3.865   3.381  1.00  0.00           H  
HETATM   98  H22 UNL     1      -0.878  -3.426   4.319  1.00  0.00           H  
HETATM   99  H23 UNL     1       0.187  -2.092   4.831  1.00  0.00           H  
HETATM  100  H24 UNL     1      -2.828   0.044   2.108  1.00  0.00           H  
HETATM  101  H25 UNL     1      -4.191   0.584   4.736  1.00  0.00           H  
HETATM  102  H26 UNL     1      -5.863   2.340   4.603  1.00  0.00           H  
HETATM  103  H27 UNL     1      -7.325   3.872   3.351  1.00  0.00           H  
HETATM  104  H28 UNL     1      -8.063   4.771   1.332  1.00  0.00           H  
HETATM  105  H29 UNL     1      -6.099   3.209  -1.123  1.00  0.00           H  
HETATM  106  H30 UNL     1      -4.109   1.054   0.993  1.00  0.00           H  
HETATM  107  H31 UNL     1      -0.805  -4.083   2.010  1.00  0.00           H  
HETATM  108  H32 UNL     1       0.804  -5.299   1.359  1.00  0.00           H  
HETATM  109  H33 UNL     1      -0.283  -2.813  -0.268  1.00  0.00           H  
HETATM  110  H34 UNL     1      -2.130  -3.180   1.077  1.00  0.00           H  
HETATM  111  H35 UNL     1       0.033  -0.364   1.645  1.00  0.00           H  
HETATM  112  H36 UNL     1       0.957   1.012   0.812  1.00  0.00           H  
HETATM  113  H37 UNL     1       0.034   2.131   1.483  1.00  0.00           H  
HETATM  114  H38 UNL     1      -1.205   4.335   1.501  1.00  0.00           H  
HETATM  115  H39 UNL     1      -2.221   2.902   1.510  1.00  0.00           H  
HETATM  116  H40 UNL     1      -2.873   4.918  -2.775  1.00  0.00           H  
HETATM  117  H41 UNL     1      -4.209   6.182  -4.377  1.00  0.00           H  
HETATM  118  H42 UNL     1      -6.028   8.705  -4.034  1.00  0.00           H  
HETATM  119  H43 UNL     1      -6.653   7.682  -1.290  1.00  0.00           H  
HETATM  120  H44 UNL     1      -5.341   6.432   0.374  1.00  0.00           H  
HETATM  121  H45 UNL     1       0.528   4.491  -0.139  1.00  0.00           H  
HETATM  122  H46 UNL     1       2.410   4.399   1.050  1.00  0.00           H  
HETATM  123  H47 UNL     1       1.219   3.362  -2.022  1.00  0.00           H  
HETATM  124  H48 UNL     1       3.509   3.016  -1.796  1.00  0.00           H  
HETATM  125  H49 UNL     1       2.710   1.057  -0.934  1.00  0.00           H  
HETATM  126  H50 UNL     1       0.641   0.448  -2.568  1.00  0.00           H  
HETATM  127  H51 UNL     1       5.180   1.849   0.176  1.00  0.00           H  
HETATM  128  H52 UNL     1       5.100   3.274   2.098  1.00  0.00           H  
HETATM  129  H53 UNL     1       4.402   2.099   5.514  1.00  0.00           H  
CONECT    1    2   77   78   79
CONECT    2    3
CONECT    3    4    4   75
CONECT    4    5   80
CONECT    5    6   73   73
CONECT    6    7    7   28
CONECT    7    8
CONECT    8    9    9   26
CONECT    9   10   81
CONECT   10   11   12   12
CONECT   11   82
CONECT   12   13   83
CONECT   13   14   26   26
CONECT   14   15
CONECT   15   16   24   84
CONECT   16   17
CONECT   17   18   20   85
CONECT   18   19   86   87
CONECT   19   88
CONECT   20   21   22   89
CONECT   21   90
CONECT   22   23   24   91
CONECT   23   92
CONECT   24   25   93
CONECT   25   94
CONECT   26   27
CONECT   27   28   28   95
CONECT   28   29
CONECT   29   30
CONECT   30   31   51   96
CONECT   31   32
CONECT   32   33   47   97
CONECT   33   34   98   99
CONECT   34   35
CONECT   35   36   36   37
CONECT   37   38   38  100
CONECT   38   39  101
CONECT   39   40   40   46
CONECT   40   41  102
CONECT   41   42   42  103
CONECT   42   43   44
CONECT   43  104
CONECT   44   45   46   46
CONECT   45  105
CONECT   46  106
CONECT   47   48   49  107
CONECT   48  108
CONECT   49   50   51  109
CONECT   50  110
CONECT   51   52  111
CONECT   52   53
CONECT   53   54   71  112
CONECT   54   55
CONECT   55   56   67  113
CONECT   56   57  114  115
CONECT   57   58
CONECT   58   59   59   60
CONECT   60   61   61   66
CONECT   61   62  116
CONECT   62   63   63  117
CONECT   63   64   65
CONECT   64  118
CONECT   65   66   66  119
CONECT   66  120
CONECT   67   68   69  121
CONECT   68  122
CONECT   69   70   71  123
CONECT   70  124
CONECT   71   72  125
CONECT   72  126
CONECT   73   74  127
CONECT   74   75   75  128
CONECT   75   76
CONECT   76  129
END
Download

SMILES for HMDB0035454 (YGM 5A)

COC1=C(O)C=CC(=C1)C1=[O+]C2=C(C=C1OC1OC(COC(=O)\C=C\C3=CC=C(O)C(O)=C3)C(O)C(O)C1OC1OC(COC(=O)C3=CC=C(O)C=C3)C(O)C(O)C1O)C(OC1OC(CO)C(O)C(O)C1O)=CC(O)=C2
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INCHI for HMDB0035454 (YGM 5A)

InChI=1S/C50H52O26/c1-67-31-13-22(6-10-27(31)55)45-32(16-25-29(70-45)14-24(53)15-30(25)71-48-43(64)40(61)37(58)33(17-51)73-48)72-50-46(42(63)39(60)34(75-50)18-68-36(57)11-3-20-2-9-26(54)28(56)12-20)76-49-44(65)41(62)38(59)35(74-49)19-69-47(66)21-4-7-23(52)8-5-21/h2-16,33-35,37-44,46,48-51,58-65H,17-19H2,1H3,(H4-,52,53,54,55,56,57,66)/p+1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC50H53O26
Average Molecular Weight1069.9402
Monoisotopic Molecular Weight1069.282506868
IUPAC Name3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-({3,4,5-trihydroxy-6-[(4-hydroxybenzoyloxy)methyl]oxan-2-yl}oxy)oxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
Traditional Name3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-({3,4,5-trihydroxy-6-[(4-hydroxybenzoyloxy)methyl]oxan-2-yl}oxy)oxan-2-yl]oxy}-7-hydroxy-2-(4-hydroxy-3-methoxyphenyl)-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
CAS Registry NumberNot Available
SMILES
COC1=C(O)C=CC(=C1)C1=[O+]C2=C(C=C1OC1OC(COC(=O)\C=C\C3=CC=C(O)C(O)=C3)C(O)C(O)C1OC1OC(COC(=O)C3=CC=C(O)C=C3)C(O)C(O)C1O)C(OC1OC(CO)C(O)C(O)C1O)=CC(O)=C2
InChI Identifier
InChI=1S/C50H52O26/c1-67-31-13-22(6-10-27(31)55)45-32(16-25-29(70-45)14-24(53)15-30(25)71-48-43(64)40(61)37(58)33(17-51)73-48)72-50-46(42(63)39(60)34(75-50)18-68-36(57)11-3-20-2-9-26(54)28(56)12-20)76-49-44(65)41(62)38(59)35(74-49)19-69-47(66)21-4-7-23(52)8-5-21/h2-16,33-35,37-44,46,48-51,58-65H,17-19H2,1H3,(H4-,52,53,54,55,56,57,66)/p+1
InChI KeyDYZALFMOLIKHGK-UHFFFAOYSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as anthocyanidin 3-o-6-p-coumaroyl glycosides. These are anthocyanidin 3-O-glycosides where the carbohydrate moiety is esterified at the C6 position with a p-coumaric acid. P-coumaric acid is an organic derivative of cinnamic acid, that carries a hydroxyl group at the 4-position of the benzene ring.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassFlavonoids
Sub ClassFlavonoid glycosides
Direct ParentAnthocyanidin 3-O-6-p-coumaroyl glycosides
Alternative Parents
Substituents
  • Anthocyanidin 3-o-6-p-coumaroyl-glycoside
  • Anthocyanidin-3-o-glycoside
  • Anthocyanin
  • Anthocyanidin-5-o-glycoside
  • Flavonoid-3-o-glycoside
  • 3p-methoxyflavonoid-skeleton
  • Hydroxyflavonoid
  • 4'-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Anthocyanidin
  • Phenolic glycoside
  • Cinnamic acid or derivatives
  • Coumaric acid or derivatives
  • Hydroxycinnamic acid or derivatives
  • Cinnamic acid ester
  • Disaccharide
  • Glycosyl compound
  • P-hydroxybenzoic acid ester
  • O-glycosyl compound
  • P-hydroxybenzoic acid alkyl ester
  • Benzoate ester
  • Benzopyran
  • Methoxyphenol
  • 1-benzopyran
  • Benzoic acid or derivatives
  • Styrene
  • Phenoxy compound
  • Phenol ether
  • Benzoyl
  • Catechol
  • Methoxybenzene
  • Anisole
  • Phenol
  • 1-hydroxy-4-unsubstituted benzenoid
  • Alkyl aryl ether
  • 1-hydroxy-2-unsubstituted benzenoid
  • Fatty acid ester
  • Dicarboxylic acid or derivatives
  • Fatty acyl
  • Oxane
  • Monocyclic benzene moiety
  • Benzenoid
  • Heteroaromatic compound
  • Enoate ester
  • Alpha,beta-unsaturated carboxylic ester
  • Secondary alcohol
  • Carboxylic acid ester
  • Acetal
  • Polyol
  • Ether
  • Organoheterocyclic compound
  • Oxacycle
  • Carboxylic acid derivative
  • Organic oxide
  • Organic oxygen compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Carbonyl group
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.24 g/LALOGPS
logP2.24ALOGPS
logP1.24ChemAxon
logS-3.7ALOGPS
pKa (Strongest Acidic)6.65ChemAxon
pKa (Strongest Basic)-3.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area413.57 ŲChemAxon
Rotatable Bond Count18ChemAxon
Refractivity260.63 m³·mol⁻¹ChemAxon
Polarizability103 ųChemAxon
Number of Rings8ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+316.5530932474
DeepCCS[M-H]-314.82730932474
DeepCCS[M-2H]-348.86130932474
DeepCCS[M+Na]+322.78930932474
AllCCS[M+H]+296.432859911
AllCCS[M+H-H2O]+297.232859911
AllCCS[M+NH4]+295.632859911
AllCCS[M+Na]+295.432859911
AllCCS[M-H]-274.832859911
AllCCS[M+Na-2H]-280.232859911
AllCCS[M+HCOO]-286.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.3.84 minutes32390414
Predicted by Siyang on May 30, 202214.0808 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.83 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid311.0 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2452.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid202.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid184.4 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid208.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid120.6 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid456.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid503.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)944.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid922.8 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid563.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1434.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid339.6 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid368.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate434.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA555.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water254.4 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 10V, Positive-QTOFsplash10-00di-9100000000-b228c2de46ce1516d3302016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 20V, Positive-QTOFsplash10-00kr-9200000000-14f76c4437b41ace7d9e2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 40V, Positive-QTOFsplash10-03dj-7900000001-fba71449d36eb5055e392016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 10V, Negative-QTOFsplash10-014i-9200000000-4ecdda524cd7847f60b82016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 20V, Negative-QTOFsplash10-00lr-9400000000-c9849b313f1486b78e7b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 40V, Negative-QTOFsplash10-052f-9200000000-84eb3a7a172f14b7787d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 10V, Positive-QTOFsplash10-03xr-6900411500-817a7ba28691b400d4512021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 20V, Positive-QTOFsplash10-02ti-5401405900-04f139c8440ea1987b332021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 5A 40V, Positive-QTOFsplash10-02ms-1900000100-10932e21be6359973c4f2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB014138
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131751764
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details
1. Liver carboxylesterase 1
General function:
Lipid transport and metabolism
Specific function:
Involved in the detoxification of xenobiotics and in the activation of ester and amide prodrugs. Hydrolyzes aromatic and aliphatic esters, but has no catalytic activity toward amides or a fatty acyl-CoA ester. Hydrolyzes the methyl ester group of cocaine to form benzoylecgonine. Catalyzes the transesterification of cocaine to form cocaethylene. Displays fatty acid ethyl ester synthase activity, catalyzing the ethyl esterification of oleic acid to ethyloleate.
Gene Name:
CES1
Uniprot ID:
P23141
Molecular weight:
62520.62
Reactions
YGM 5A → YGM 5Bdetails