Hmdb loader

Showing metabocard for YGM 3 (HMDB0035461)

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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 20:27:12 UTC
Update Date2022-03-07 02:54:31 UTC
HMDB IDHMDB0035461
Secondary Accession Numbers
  • HMDB35461
Metabolite Identification
Common NameYGM 3
DescriptionYGM 3 belongs to the class of organic compounds known as flavonoid 3-o-p-coumaroyl glycosides. These are flavonoid 3-O-glycosides where the carbohydrate moiety is esterified 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 3 has been detected, but not quantified in, a few different foods, such as breakfast cereal, cereals and cereal products, and root vegetables. This could make YGM 3 a potential biomarker for the consumption of these foods. Based on a literature review a significant number of articles have been published on YGM 3.
Structure
Data?1563862723
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0035461 (YGM 3)


  Mrv0541 05061308292D          

 79 86  0  0  0  0            999 V2000
   10.7171    8.6625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0026    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7171    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2881    7.0125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.2881    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 79 51  1  0  0  0  0
M  CHG  1  73   1
M  END
Download

3D MOL for HMDB0035461 (YGM 3)

HMDB0035461
     RDKit          3D
YGM 3
134141  0  0  0  0  0  0  0  0999 V2000
   -1.3088   -2.1756    4.8260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0828   -1.4328    5.9611 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4558   -0.2456    6.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1196    0.5331    5.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7533    1.7168    5.3698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3758    2.5376    4.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3862    2.3629    3.0582 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0719    3.2819    2.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6964    4.2781    2.6389 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0753    3.1007    0.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7942    3.9680   -0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6223    3.5808   -1.4762 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9043    2.2501   -1.7823 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0464    1.8223   -1.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1482    0.4471   -1.3797 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4968   -0.3243   -0.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3653   -1.1249   -1.0697 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7601   -0.6829   -2.1750 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6159   -0.4040   -2.7570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5791   -0.3133   -2.0158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7946   -0.0245   -2.5894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9685    0.0794   -1.8729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9654   -0.0993   -0.5178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0788   -0.0028    0.3254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2705    1.3664    0.6883 O   0  0  0  0  0  0  0  0  0  0  0  0
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    0.4777   -0.1833   -4.1073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5935   -0.2289   -5.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3132    0.1376   -6.3680 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3067    0.0937   -7.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5771   -0.3045   -6.9870 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5296   -0.3275   -7.9763 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8753   -0.6693   -5.7055 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1482   -1.0781   -5.3430 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8631   -0.6287   -4.7316 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3676   -3.2655    1.6806 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4066   -3.9190    0.8375 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5681   -4.7626    1.3484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5792   -4.9265    2.5913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5409   -5.4304    0.4518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4893   -5.2337   -0.8454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3421   -5.7971   -1.8500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3536   -6.6639   -1.5426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1838   -7.2150   -2.5225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9910   -6.8820   -3.8644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8450   -7.4573   -4.8037 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9804   -6.0155   -4.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7661   -5.6687   -5.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1689   -5.4819   -3.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5136   -2.0298    1.3039 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3739   -1.3695    2.5172 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3778   -1.1679    0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1616   -2.0488   -0.3653 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2156    2.6494   -1.2537 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1584    1.8996   -2.0181 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0560    3.9533   -1.9759 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  1  40   1
M  END
Download

3D SDF for HMDB0035461 (YGM 3)


  Mrv0541 05061308292D          

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 73 48  1  0  0  0  0
 74 32  1  0  0  0  0
 74 50  1  0  0  0  0
 75 34  1  0  0  0  0
 75 52  1  0  0  0  0
 76 35  1  0  0  0  0
 76 50  1  0  0  0  0
 77 36  1  0  0  0  0
 77 51  1  0  0  0  0
 78 37  1  0  0  0  0
 78 52  1  0  0  0  0
 79 49  1  0  0  0  0
 79 51  1  0  0  0  0
M  CHG  1  73   1
M  END
> <DATABASE_ID>
HMDB0035461

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C=CC(\C=C\C(=O)OCC2OC(OC3C(OC4=C([O+]=C5C=C(O)C=C(OC6OC(CO)C(O)C(O)C6O)C5=C4)C4=CC(O)=C(O)C=C4)OC(COC(=O)\C=C\C4=CC(O)=C(O)C=C4)C(O)C3O)C(O)C(O)C2O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C52H54O27/c1-70-33-13-22(3-8-28(33)57)5-11-39(61)71-19-36-41(63)44(66)47(69)51(77-36)79-49-45(67)42(64)37(20-72-38(60)10-4-21-2-7-26(55)29(58)12-21)78-52(49)75-34-17-25-31(73-48(34)23-6-9-27(56)30(59)14-23)15-24(54)16-32(25)74-50-46(68)43(65)40(62)35(18-53)76-50/h2-17,35-37,40-47,49-53,62-69H,18-20H2,1H3,(H5-,54,55,56,57,58,59,60,61)/p+1

> <INCHI_KEY>
CSWCMIODPBATKN-UHFFFAOYSA-O

> <FORMULA>
C52H55O27

> <MOLECULAR_WEIGHT>
1111.9769

> <EXACT_MASS>
1111.293071554

> <JCHEM_ACCEPTOR_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
107.74266414852522

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
15

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
2.38

> <JCHEM_LOGP>
1.8972999999999975

> <ALOGPS_LOGS>
-3.88

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
7.961981040265136

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.64673672977349

> <JCHEM_PKA_STRONGEST_BASIC>
-3.9477724927082933

> <JCHEM_POLAR_SURFACE_AREA>
433.8000000000002

> <JCHEM_REFRACTIVITY>
272.3565

> <JCHEM_ROTATABLE_BOND_COUNT>
19

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.50e-01 g/l

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

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0035461 (YGM 3)

HMDB0035461
     RDKit          3D
YGM 3
134141  0  0  0  0  0  0  0  0999 V2000
   -1.3088   -2.1756    4.8260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0828   -1.4328    5.9611 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4558   -0.2456    6.1610 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1196    0.5331    5.1723 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7533    1.7168    5.3698 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3758    2.5376    4.3741 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3862    2.3629    3.0582 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0719    3.2819    2.1740 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6964    4.2781    2.6389 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0753    3.1007    0.8104 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7942    3.9680   -0.0471 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6223    3.5808   -1.4762 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9043    2.2501   -1.7823 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0464    1.8223   -1.0590 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1482    0.4471   -1.3797 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4968   -0.3243   -0.4812 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3653   -1.1249   -1.0697 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7601   -0.6829   -2.1750 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6159   -0.4040   -2.7570 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5791   -0.3133   -2.0158 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7946   -0.0245   -2.5894 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9685    0.0794   -1.8729 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9654   -0.0993   -0.5178 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0788   -0.0028    0.3254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2705    1.3664    0.6883 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2568    1.4529    1.6660 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8113    2.8697    1.7405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8004    3.7757    2.0664 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5592    1.1462    2.9900 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4642    0.7737    3.9647 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4903    0.1217    2.7261 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3023    0.7693    2.3892 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8395   -0.8121    1.5685 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7362   -1.6410    1.3751 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1437    0.3742   -2.5231 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1942    0.5773   -3.8941 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4040    0.8734   -4.5215 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.8334    0.1816   -3.9591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7225    0.0915   -4.6170 O   0  0  0  0  0  3  0  0  0  0  0  0
    0.4777   -0.1833   -4.1073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5935   -0.2289   -5.0584 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3132    0.1376   -6.3680 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3067    0.0937   -7.3073 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5771   -0.3045   -6.9870 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5296   -0.3275   -7.9763 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8753   -0.6693   -5.7055 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1482   -1.0781   -5.3430 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8631   -0.6287   -4.7316 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5119   -1.4871    0.0336 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2273   -2.4644    0.7188 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3676   -3.2655    1.6806 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4066   -3.9190    0.8375 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5681   -4.7626    1.3484 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5792   -4.9265    2.5913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5409   -5.4304    0.4518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4893   -5.2337   -0.8454 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3421   -5.7971   -1.8500 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3536   -6.6639   -1.5426 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1838   -7.2150   -2.5225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9910   -6.8820   -3.8644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8450   -7.4573   -4.8037 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9804   -6.0155   -4.1773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7661   -5.6687   -5.4964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1689   -5.4819   -3.1811 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5136   -2.0298    1.3039 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3739   -1.3695    2.5172 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3778   -1.1679    0.3739 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1616   -2.0488   -0.3653 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2156    2.6494   -1.2537 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1584    1.8996   -2.0181 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0560    3.9533   -1.9759 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6669    4.9487   -1.1755 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6741    4.4231   -2.2602 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8055    2.1521    6.7041 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2484    1.4155    7.7155 C   0  0  0  0  0  0  0  0  0  0  0  0
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 11 86  1  0
 11 87  1  0
 12 88  1  0
 14 89  1  0
 16 90  1  0
 17 91  1  0
 20 92  1  0
 24 93  1  0
 26 94  1  0
 27 95  1  0
 27 96  1  0
 28 97  1  0
 29 98  1  0
 30 99  1  0
 31100  1  0
 32101  1  0
 33102  1  0
 34103  1  0
 35104  1  0
 37105  1  0
 38106  1  0
 43107  1  0
 44108  1  0
 46109  1  0
 48110  1  0
 49111  1  0
 51112  1  0
 52113  1  0
 52114  1  0
 56115  1  0
 57116  1  0
 59117  1  0
 60118  1  0
 62119  1  0
 64120  1  0
 65121  1  0
 66122  1  0
 67123  1  0
 68124  1  0
 69125  1  0
 70126  1  0
 71127  1  0
 72128  1  0
 73129  1  0
 74130  1  0
 75131  1  0
 76132  1  0
 77133  1  0
 79134  1  0
M  CHG  1  40   1
M  END
Download

PDB for HMDB0035461 (YGM 3)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0      20.005  16.170   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.001  11.550   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.672  10.780   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      16.004  10.780   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  13.090   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.005  11.550   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.336  -5.390   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      16.004   9.240   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  11.550   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      17.338  13.090   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.336  -2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.667   1.540   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      17.338  11.550   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       2.667  13.860   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      10.669  -4.620   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      20.005  13.090   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       1.334  13.090   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.669  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      18.672  13.860   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      13.337   4.620   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       6.668   3.850   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      14.671   8.470   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      14.671   3.850   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       8.002   4.620   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      14.671   2.310   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       9.336   3.850   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      13.337   1.540   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       9.336   2.310   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      12.003   2.310   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      -2.667   0.000   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0       0.000  -3.080   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0       2.667  15.400   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      12.003  -5.390   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      21.339  13.860   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0       0.000  13.860   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      12.003  -2.310   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      13.337   9.240   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      16.004   4.620   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0       8.002   6.160   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       0.000   6.160   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      16.004   1.540   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      13.337   0.000   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      18.672  15.400   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0      14.671   6.930   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0       5.335   6.160   0.000  0.00  0.00           O+0
HETATM   73  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O+1
HETATM   74  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O+0
HETATM   76  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   77  O   UNK     0      12.003   3.850   0.000  0.00  0.00           O+0
HETATM   78  O   UNK     0       6.668   2.310   0.000  0.00  0.00           O+0
HETATM   79  O   UNK     0      10.669   1.540   0.000  0.00  0.00           O+0
CONECT    1   70                                                            
CONECT    2    7   21                                                       
CONECT    3    8   22                                                       
CONECT    4   10   21                                                       
CONECT    5   11   22                                                       
CONECT    6    9   23                                                       
CONECT    7    2   26                                                       
CONECT    8    3   28                                                       
CONECT    9    6   27                                                       
CONECT   10    4   38                                                       
CONECT   11    5   39                                                       
CONECT   12   21   29                                                       
CONECT   13   22   33                                                       
CONECT   14   23   30                                                       
CONECT   15   24   31                                                       
CONECT   16   24   32                                                       
CONECT   17   25   34                                                       
CONECT   18   35   53                                                       
CONECT   19   36   71                                                       
CONECT   20   37   72                                                       
CONECT   21    2    4   12                                                  
CONECT   22    3    5   13                                                  
CONECT   23    6   14   48                                                  
CONECT   24   15   16   54                                                  
CONECT   25   17   31   32                                                  
CONECT   26    7   29   55                                                  
CONECT   27    9   30   56                                                  
CONECT   28    8   33   57                                                  
CONECT   29   12   26   58                                                  
CONECT   30   14   27   59                                                  
CONECT   31   15   25   73                                                  
CONECT   32   16   25   74                                                  
CONECT   33   13   28   70                                                  
CONECT   34   17   48   75                                                  
CONECT   35   18   40   76                                                  
CONECT   36   19   41   77                                                  
CONECT   37   20   42   78                                                  
CONECT   38   10   60   72                                                  
CONECT   39   11   61   71                                                  
CONECT   40   35   43   62                                                  
CONECT   41   36   44   63                                                  
CONECT   42   37   45   64                                                  
CONECT   43   40   46   65                                                  
CONECT   44   41   47   66                                                  
CONECT   45   42   49   67                                                  
CONECT   46   43   50   68                                                  
CONECT   47   44   51   69                                                  
CONECT   48   23   34   73                                                  
CONECT   49   45   52   79                                                  
CONECT   50   46   74   76                                                  
CONECT   51   47   77   79                                                  
CONECT   52   49   75   78                                                  
CONECT   53   18                                                            
CONECT   54   24                                                            
CONECT   55   26                                                            
CONECT   56   27                                                            
CONECT   57   28                                                            
CONECT   58   29                                                            
CONECT   59   30                                                            
CONECT   60   38                                                            
CONECT   61   39                                                            
CONECT   62   40                                                            
CONECT   63   41                                                            
CONECT   64   42                                                            
CONECT   65   43                                                            
CONECT   66   44                                                            
CONECT   67   45                                                            
CONECT   68   46                                                            
CONECT   69   47                                                            
CONECT   70    1   33                                                       
CONECT   71   19   39                                                       
CONECT   72   20   38                                                       
CONECT   73   31   48                                                       
CONECT   74   32   50                                                       
CONECT   75   34   52                                                       
CONECT   76   35   50                                                       
CONECT   77   36   51                                                       
CONECT   78   37   52                                                       
CONECT   79   49   51                                                       
MASTER        0    0    0    0    0    0    0    0   79    0  172    0
END
Download

3D PDB for HMDB0035461 (YGM 3)

COMPND    HMDB0035461
HETATM    1  C1  UNL     1      -1.309  -2.176   4.826  1.00  0.00           C  
HETATM    2  O1  UNL     1      -1.083  -1.433   5.961  1.00  0.00           O  
HETATM    3  C2  UNL     1      -0.456  -0.246   6.161  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.120   0.533   5.172  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.753   1.717   5.370  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.376   2.538   4.374  1.00  0.00           C  
HETATM    7  C6  UNL     1       1.386   2.363   3.058  1.00  0.00           C  
HETATM    8  C7  UNL     1       2.072   3.282   2.174  1.00  0.00           C  
HETATM    9  O2  UNL     1       2.696   4.278   2.639  1.00  0.00           O  
HETATM   10  O3  UNL     1       2.075   3.101   0.810  1.00  0.00           O  
HETATM   11  C8  UNL     1       2.794   3.968  -0.047  1.00  0.00           C  
HETATM   12  C9  UNL     1       2.622   3.581  -1.476  1.00  0.00           C  
HETATM   13  O4  UNL     1       2.904   2.250  -1.782  1.00  0.00           O  
HETATM   14  C10 UNL     1       4.046   1.822  -1.059  1.00  0.00           C  
HETATM   15  O5  UNL     1       4.148   0.447  -1.380  1.00  0.00           O  
HETATM   16  C11 UNL     1       3.497  -0.324  -0.481  1.00  0.00           C  
HETATM   17  C12 UNL     1       2.365  -1.125  -1.070  1.00  0.00           C  
HETATM   18  O6  UNL     1       1.760  -0.683  -2.175  1.00  0.00           O  
HETATM   19  C13 UNL     1       0.616  -0.404  -2.757  1.00  0.00           C  
HETATM   20  C14 UNL     1      -0.579  -0.313  -2.016  1.00  0.00           C  
HETATM   21  C15 UNL     1      -1.795  -0.025  -2.589  1.00  0.00           C  
HETATM   22  C16 UNL     1      -2.968   0.079  -1.873  1.00  0.00           C  
HETATM   23  O7  UNL     1      -2.965  -0.099  -0.518  1.00  0.00           O  
HETATM   24  C17 UNL     1      -4.079  -0.003   0.325  1.00  0.00           C  
HETATM   25  O8  UNL     1      -4.270   1.366   0.688  1.00  0.00           O  
HETATM   26  C18 UNL     1      -5.257   1.453   1.666  1.00  0.00           C  
HETATM   27  C19 UNL     1      -5.811   2.870   1.740  1.00  0.00           C  
HETATM   28  O9  UNL     1      -4.800   3.776   2.066  1.00  0.00           O  
HETATM   29  C20 UNL     1      -4.559   1.146   2.990  1.00  0.00           C  
HETATM   30  O10 UNL     1      -5.464   0.774   3.965  1.00  0.00           O  
HETATM   31  C21 UNL     1      -3.490   0.122   2.726  1.00  0.00           C  
HETATM   32  O11 UNL     1      -2.302   0.769   2.389  1.00  0.00           O  
HETATM   33  C22 UNL     1      -3.839  -0.812   1.568  1.00  0.00           C  
HETATM   34  O12 UNL     1      -2.736  -1.641   1.375  1.00  0.00           O  
HETATM   35  C23 UNL     1      -4.144   0.374  -2.523  1.00  0.00           C  
HETATM   36  C24 UNL     1      -4.194   0.577  -3.894  1.00  0.00           C  
HETATM   37  O13 UNL     1      -5.404   0.873  -4.522  1.00  0.00           O  
HETATM   38  C25 UNL     1      -3.032   0.480  -4.610  1.00  0.00           C  
HETATM   39  C26 UNL     1      -1.833   0.182  -3.959  1.00  0.00           C  
HETATM   40  O14 UNL     1      -0.723   0.091  -4.617  1.00  0.00           O1+
HETATM   41  C27 UNL     1       0.478  -0.183  -4.107  1.00  0.00           C  
HETATM   42  C28 UNL     1       1.593  -0.229  -5.058  1.00  0.00           C  
HETATM   43  C29 UNL     1       1.313   0.138  -6.368  1.00  0.00           C  
HETATM   44  C30 UNL     1       2.307   0.094  -7.307  1.00  0.00           C  
HETATM   45  C31 UNL     1       3.577  -0.304  -6.987  1.00  0.00           C  
HETATM   46  O15 UNL     1       4.530  -0.327  -7.976  1.00  0.00           O  
HETATM   47  C32 UNL     1       3.875  -0.669  -5.706  1.00  0.00           C  
HETATM   48  O16 UNL     1       5.148  -1.078  -5.343  1.00  0.00           O  
HETATM   49  C33 UNL     1       2.863  -0.629  -4.732  1.00  0.00           C  
HETATM   50  O17 UNL     1       1.512  -1.487   0.034  1.00  0.00           O  
HETATM   51  C34 UNL     1       2.227  -2.464   0.719  1.00  0.00           C  
HETATM   52  C35 UNL     1       1.368  -3.265   1.681  1.00  0.00           C  
HETATM   53  O18 UNL     1       0.407  -3.919   0.837  1.00  0.00           O  
HETATM   54  C36 UNL     1      -0.568  -4.763   1.348  1.00  0.00           C  
HETATM   55  O19 UNL     1      -0.579  -4.927   2.591  1.00  0.00           O  
HETATM   56  C37 UNL     1      -1.541  -5.430   0.452  1.00  0.00           C  
HETATM   57  C38 UNL     1      -1.489  -5.234  -0.845  1.00  0.00           C  
HETATM   58  C39 UNL     1      -2.342  -5.797  -1.850  1.00  0.00           C  
HETATM   59  C40 UNL     1      -3.354  -6.664  -1.543  1.00  0.00           C  
HETATM   60  C41 UNL     1      -4.184  -7.215  -2.523  1.00  0.00           C  
HETATM   61  C42 UNL     1      -3.991  -6.882  -3.864  1.00  0.00           C  
HETATM   62  O20 UNL     1      -4.845  -7.457  -4.804  1.00  0.00           O  
HETATM   63  C43 UNL     1      -2.980  -6.015  -4.177  1.00  0.00           C  
HETATM   64  O21 UNL     1      -2.766  -5.669  -5.496  1.00  0.00           O  
HETATM   65  C44 UNL     1      -2.169  -5.482  -3.181  1.00  0.00           C  
HETATM   66  C45 UNL     1       3.514  -2.030   1.304  1.00  0.00           C  
HETATM   67  O22 UNL     1       3.374  -1.370   2.517  1.00  0.00           O  
HETATM   68  C46 UNL     1       4.378  -1.168   0.374  1.00  0.00           C  
HETATM   69  O23 UNL     1       5.162  -2.049  -0.365  1.00  0.00           O  
HETATM   70  C47 UNL     1       5.216   2.649  -1.254  1.00  0.00           C  
HETATM   71  O24 UNL     1       6.158   1.900  -2.018  1.00  0.00           O  
HETATM   72  C48 UNL     1       5.056   3.953  -1.976  1.00  0.00           C  
HETATM   73  O25 UNL     1       5.667   4.949  -1.175  1.00  0.00           O  
HETATM   74  C49 UNL     1       3.674   4.423  -2.260  1.00  0.00           C  
HETATM   75  O26 UNL     1       3.451   5.741  -1.875  1.00  0.00           O  
HETATM   76  C50 UNL     1       0.806   2.152   6.704  1.00  0.00           C  
HETATM   77  C51 UNL     1       0.248   1.415   7.716  1.00  0.00           C  
HETATM   78  C52 UNL     1      -0.387   0.217   7.475  1.00  0.00           C  
HETATM   79  O27 UNL     1      -0.947  -0.522   8.503  1.00  0.00           O  
HETATM   80  H1  UNL     1      -2.366  -2.411   4.608  1.00  0.00           H  
HETATM   81  H2  UNL     1      -0.854  -1.788   3.893  1.00  0.00           H  
HETATM   82  H3  UNL     1      -0.833  -3.200   4.980  1.00  0.00           H  
HETATM   83  H4  UNL     1       0.048   0.149   4.153  1.00  0.00           H  
HETATM   84  H5  UNL     1       1.929   3.440   4.688  1.00  0.00           H  
HETATM   85  H6  UNL     1       0.857   1.501   2.687  1.00  0.00           H  
HETATM   86  H7  UNL     1       2.391   5.025   0.037  1.00  0.00           H  
HETATM   87  H8  UNL     1       3.853   4.065   0.249  1.00  0.00           H  
HETATM   88  H9  UNL     1       1.657   3.839  -1.899  1.00  0.00           H  
HETATM   89  H10 UNL     1       3.666   1.841  -0.012  1.00  0.00           H  
HETATM   90  H11 UNL     1       3.014   0.398   0.263  1.00  0.00           H  
HETATM   91  H12 UNL     1       2.775  -2.170  -1.310  1.00  0.00           H  
HETATM   92  H13 UNL     1      -0.555  -0.475  -0.954  1.00  0.00           H  
HETATM   93  H14 UNL     1      -4.995  -0.299  -0.204  1.00  0.00           H  
HETATM   94  H15 UNL     1      -6.116   0.781   1.483  1.00  0.00           H  
HETATM   95  H16 UNL     1      -6.562   2.883   2.554  1.00  0.00           H  
HETATM   96  H17 UNL     1      -6.338   3.137   0.805  1.00  0.00           H  
HETATM   97  H18 UNL     1      -5.003   4.690   1.807  1.00  0.00           H  
HETATM   98  H19 UNL     1      -4.108   2.129   3.298  1.00  0.00           H  
HETATM   99  H20 UNL     1      -5.445   1.413   4.731  1.00  0.00           H  
HETATM  100  H21 UNL     1      -3.348  -0.494   3.617  1.00  0.00           H  
HETATM  101  H22 UNL     1      -2.417   1.735   2.324  1.00  0.00           H  
HETATM  102  H23 UNL     1      -4.684  -1.481   1.839  1.00  0.00           H  
HETATM  103  H24 UNL     1      -1.889  -1.174   1.263  1.00  0.00           H  
HETATM  104  H25 UNL     1      -5.092   0.468  -2.017  1.00  0.00           H  
HETATM  105  H26 UNL     1      -6.031   0.188  -4.891  1.00  0.00           H  
HETATM  106  H27 UNL     1      -2.996   0.625  -5.674  1.00  0.00           H  
HETATM  107  H28 UNL     1       0.303   0.458  -6.623  1.00  0.00           H  
HETATM  108  H29 UNL     1       2.014   0.398  -8.323  1.00  0.00           H  
HETATM  109  H30 UNL     1       5.474  -0.616  -7.770  1.00  0.00           H  
HETATM  110  H31 UNL     1       5.357  -1.346  -4.390  1.00  0.00           H  
HETATM  111  H32 UNL     1       3.114  -0.926  -3.733  1.00  0.00           H  
HETATM  112  H33 UNL     1       2.473  -3.231  -0.099  1.00  0.00           H  
HETATM  113  H34 UNL     1       2.017  -4.020   2.140  1.00  0.00           H  
HETATM  114  H35 UNL     1       0.889  -2.628   2.430  1.00  0.00           H  
HETATM  115  H36 UNL     1      -2.300  -6.082   0.841  1.00  0.00           H  
HETATM  116  H37 UNL     1      -0.685  -4.551  -1.171  1.00  0.00           H  
HETATM  117  H38 UNL     1      -3.521  -6.937  -0.497  1.00  0.00           H  
HETATM  118  H39 UNL     1      -4.973  -7.894  -2.268  1.00  0.00           H  
HETATM  119  H40 UNL     1      -4.800  -7.298  -5.797  1.00  0.00           H  
HETATM  120  H41 UNL     1      -3.317  -6.018  -6.263  1.00  0.00           H  
HETATM  121  H42 UNL     1      -1.372  -4.798  -3.442  1.00  0.00           H  
HETATM  122  H43 UNL     1       4.105  -2.971   1.531  1.00  0.00           H  
HETATM  123  H44 UNL     1       3.807  -1.851   3.271  1.00  0.00           H  
HETATM  124  H45 UNL     1       5.041  -0.577   1.010  1.00  0.00           H  
HETATM  125  H46 UNL     1       5.987  -1.549  -0.663  1.00  0.00           H  
HETATM  126  H47 UNL     1       5.802   2.816  -0.288  1.00  0.00           H  
HETATM  127  H48 UNL     1       5.718   1.562  -2.849  1.00  0.00           H  
HETATM  128  H49 UNL     1       5.628   3.993  -2.931  1.00  0.00           H  
HETATM  129  H50 UNL     1       6.628   5.049  -1.391  1.00  0.00           H  
HETATM  130  H51 UNL     1       3.421   4.348  -3.339  1.00  0.00           H  
HETATM  131  H52 UNL     1       2.482   5.923  -2.106  1.00  0.00           H  
HETATM  132  H53 UNL     1       1.291   3.082   6.955  1.00  0.00           H  
HETATM  133  H54 UNL     1       0.295   1.760   8.767  1.00  0.00           H  
HETATM  134  H55 UNL     1      -0.878  -0.149   9.442  1.00  0.00           H  
CONECT    1    2   80   81   82
CONECT    2    3
CONECT    3    4    4   78
CONECT    4    5   83
CONECT    5    6   76   76
CONECT    6    7    7   84
CONECT    7    8   85
CONECT    8    9    9   10
CONECT   10   11
CONECT   11   12   86   87
CONECT   12   13   74   88
CONECT   13   14
CONECT   14   15   70   89
CONECT   15   16
CONECT   16   17   68   90
CONECT   17   18   50   91
CONECT   18   19
CONECT   19   20   20   41
CONECT   20   21   92
CONECT   21   22   22   39
CONECT   22   23   35
CONECT   23   24
CONECT   24   25   33   93
CONECT   25   26
CONECT   26   27   29   94
CONECT   27   28   95   96
CONECT   28   97
CONECT   29   30   31   98
CONECT   30   99
CONECT   31   32   33  100
CONECT   32  101
CONECT   33   34  102
CONECT   34  103
CONECT   35   36   36  104
CONECT   36   37   38
CONECT   37  105
CONECT   38   39   39  106
CONECT   39   40
CONECT   40   41   41
CONECT   41   42
CONECT   42   43   43   49
CONECT   43   44  107
CONECT   44   45   45  108
CONECT   45   46   47
CONECT   46  109
CONECT   47   48   49   49
CONECT   48  110
CONECT   49  111
CONECT   50   51
CONECT   51   52   66  112
CONECT   52   53  113  114
CONECT   53   54
CONECT   54   55   55   56
CONECT   56   57   57  115
CONECT   57   58  116
CONECT   58   59   59   65
CONECT   59   60  117
CONECT   60   61   61  118
CONECT   61   62   63
CONECT   62  119
CONECT   63   64   65   65
CONECT   64  120
CONECT   65  121
CONECT   66   67   68  122
CONECT   67  123
CONECT   68   69  124
CONECT   69  125
CONECT   70   71   72  126
CONECT   71  127
CONECT   72   73   74  128
CONECT   73  129
CONECT   74   75  130
CONECT   75  131
CONECT   76   77  132
CONECT   77   78   78  133
CONECT   78   79
CONECT   79  134
END
Download

SMILES for HMDB0035461 (YGM 3)

COC1=C(O)C=CC(\C=C\C(=O)OCC2OC(OC3C(OC4=C([O+]=C5C=C(O)C=C(OC6OC(CO)C(O)C(O)C6O)C5=C4)C4=CC(O)=C(O)C=C4)OC(COC(=O)\C=C\C4=CC(O)=C(O)C=C4)C(O)C3O)C(O)C(O)C2O)=C1
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INCHI for HMDB0035461 (YGM 3)

InChI=1S/C52H54O27/c1-70-33-13-22(3-8-28(33)57)5-11-39(61)71-19-36-41(63)44(66)47(69)51(77-36)79-49-45(67)42(64)37(20-72-38(60)10-4-21-2-7-26(55)29(58)12-21)78-52(49)75-34-17-25-31(73-48(34)23-6-9-27(56)30(59)14-23)15-24(54)16-32(25)74-50-46(68)43(65)40(62)35(18-53)76-50/h2-17,35-37,40-47,49-53,62-69H,18-20H2,1H3,(H5-,54,55,56,57,58,59,60,61)/p+1
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC52H55O27
Average Molecular Weight1111.9769
Monoisotopic Molecular Weight1111.293071554
IUPAC Name2-(3,4-dihydroxyphenyl)-3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-{[3,4,5-trihydroxy-6-({[(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-ylium
Traditional Name2-(3,4-dihydroxyphenyl)-3-{[6-({[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}methyl)-4,5-dihydroxy-3-{[3,4,5-trihydroxy-6-({[(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-7-hydroxy-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(\C=C\C(=O)OCC2OC(OC3C(OC4=C([O+]=C5C=C(O)C=C(OC6OC(CO)C(O)C(O)C6O)C5=C4)C4=CC(O)=C(O)C=C4)OC(COC(=O)\C=C\C4=CC(O)=C(O)C=C4)C(O)C3O)C(O)C(O)C2O)=C1
InChI Identifier
InChI=1S/C52H54O27/c1-70-33-13-22(3-8-28(33)57)5-11-39(61)71-19-36-41(63)44(66)47(69)51(77-36)79-49-45(67)42(64)37(20-72-38(60)10-4-21-2-7-26(55)29(58)12-21)78-52(49)75-34-17-25-31(73-48(34)23-6-9-27(56)30(59)14-23)15-24(54)16-32(25)74-50-46(68)43(65)40(62)35(18-53)76-50/h2-17,35-37,40-47,49-53,62-69H,18-20H2,1H3,(H5-,54,55,56,57,58,59,60,61)/p+1
InChI KeyCSWCMIODPBATKN-UHFFFAOYSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as flavonoid 3-o-p-coumaroyl glycosides. These are flavonoid 3-O-glycosides where the carbohydrate moiety is esterified 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 ParentFlavonoid 3-O-p-coumaroyl glycosides
Alternative Parents
Substituents
  • Flavonoid 3-o-6-p-coumaroyl-glycoside
  • Anthocyanin
  • Anthocyanidin-5-o-glycoside
  • Anthocyanidin-3-o-glycoside
  • Flavonoid-3-o-glycoside
  • Hydroxyflavonoid
  • 3'-hydroxyflavonoid
  • 4'-hydroxyflavonoid
  • 7-hydroxyflavonoid
  • Anthocyanidin
  • Phenolic glycoside
  • Coumaric acid or derivatives
  • Hydroxycinnamic acid or derivatives
  • Cinnamic acid or derivatives
  • Cinnamic acid ester
  • Glycosyl compound
  • Disaccharide
  • O-glycosyl compound
  • Methoxyphenol
  • 1-benzopyran
  • Benzopyran
  • Methoxybenzene
  • Anisole
  • Phenoxy compound
  • Phenol ether
  • Catechol
  • Styrene
  • Fatty acid ester
  • 1-hydroxy-4-unsubstituted benzenoid
  • Phenol
  • Alkyl aryl ether
  • 1-hydroxy-2-unsubstituted benzenoid
  • Dicarboxylic acid or derivatives
  • Benzenoid
  • Oxane
  • Fatty acyl
  • Monocyclic benzene moiety
  • Heteroaromatic compound
  • Alpha,beta-unsaturated carboxylic ester
  • Enoate ester
  • Carboxylic acid ester
  • Secondary alcohol
  • Carboxylic acid derivative
  • Ether
  • Polyol
  • Acetal
  • Oxacycle
  • Organoheterocyclic compound
  • Carbonyl group
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Alcohol
  • Primary alcohol
  • 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 Solubility0.15 g/LALOGPS
logP2.38ALOGPS
logP1.9ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)6.65ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count24ChemAxon
Hydrogen Donor Count15ChemAxon
Polar Surface Area433.8 ŲChemAxon
Rotatable Bond Count19ChemAxon
Refractivity272.36 m³·mol⁻¹ChemAxon
Polarizability107.74 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]+331.52730932474
DeepCCS[M-H]-329.80330932474
DeepCCS[M-2H]-363.83630932474
DeepCCS[M+Na]+337.85630932474
AllCCS[M+H]+301.732859911
AllCCS[M+H-H2O]+302.632859911
AllCCS[M+NH4]+300.832859911
AllCCS[M+Na]+300.532859911
AllCCS[M-H]-278.832859911
AllCCS[M+Na-2H]-284.232859911
AllCCS[M+HCOO]-290.132859911

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, 2022.3.47 minutes32390414
Predicted by Siyang on May 30, 202214.1376 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.33 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid291.7 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2370.8 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid189.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid178.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid198.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid123.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid455.3 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 Acid494.1 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)911.5 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid936.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid576.3 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1381.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid322.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid350.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate405.1 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA542.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water211.9 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 10V, Positive-QTOFsplash10-03di-0900000000-99ff803b1da8d154683b2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 20V, Positive-QTOFsplash10-03fr-1900000000-a242992982340cc06d9f2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 40V, Positive-QTOFsplash10-03di-4900000000-47e302f24da9577a29242016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 10V, Negative-QTOFsplash10-03di-1900000000-fa583dd1ad047d1c7fa92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 20V, Negative-QTOFsplash10-03fr-2900000000-793596618d087b614cef2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 40V, Negative-QTOFsplash10-052f-9200000000-572b0530d2040524aa422016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 10V, Positive-QTOFsplash10-03dl-7900000003-bb3db9917e071ad95f522021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 20V, Positive-QTOFsplash10-0ir1-5400002609-3520db5ae83c7acf3a272021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - YGM 3 40V, Positive-QTOFsplash10-000j-0900000202-7a52a7605fd3d35a20292021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
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 IDFDB014146
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131751770
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 3 → 3-{[4,5-dihydroxy-6-(hydroxymethyl)-3-{[3,4,5-trihydroxy-6-({[3-(4-hydroxy-3-methoxyphenyl)prop-2-enoyl]oxy}methyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-2-(3,4-dihydroxyphenyl)-7-hydroxy-5-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-1λ⁴-chromen-1-yliumdetails