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Showing metabocard for 5-Deoxy-D-ribose (HMDB0246776)

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enzymes (4) Show 4 proteins
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-10 23:47:21 UTC
Update Date2021-10-01 18:55:26 UTC
HMDB IDHMDB0246776
Secondary Accession NumbersNone
Metabolite Identification
Common Name5-Deoxy-D-ribose
Description5-Deoxy-D-ribose belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn. Based on a literature review a significant number of articles have been published on 5-Deoxy-D-ribose. This compound has been identified in human blood as reported by (PMID: 31557052 ). 5-deoxy-d-ribose is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically 5-Deoxy-D-ribose is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0246776 (5-Deoxy-D-ribose)


  Mrv1652309112101472D          

  9  8  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  4  7  1  0  0  0  0
  3  8  1  0  0  0  0
  2  9  1  0  0  0  0
M  END
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3D MOL for HMDB0246776 (5-Deoxy-D-ribose)

HMDB0246776
     RDKit          3D
5-Deoxy-D-ribose
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.3083   -0.0009    0.5222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1240    0.0353   -0.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0388    1.3403   -0.9276 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1134   -0.1964    0.3999 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1472   -1.4701    0.9655 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3873   -0.0451   -0.4079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4603    1.1997   -1.0224 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5222   -0.2624    0.5129 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3735    0.5785    0.6659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7554   -0.9994    0.6145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0785    0.6721    0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9989    0.4525    1.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -0.7162   -1.2070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6098    1.4646   -1.7255 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0988    0.5207    1.2417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3098   -2.0745    0.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4351   -0.8179   -1.1961 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4000    1.5095   -0.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5748   -1.1904    1.0474 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
M  END
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3D SDF for HMDB0246776 (5-Deoxy-D-ribose)


  Mrv1652309112101472D          

  9  8  0  0  0  0            999 V2000
   -0.1914    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  4  7  1  0  0  0  0
  3  8  1  0  0  0  0
  2  9  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0246776

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(O)C(O)C(O)C=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3

> <INCHI_KEY>
WDRISBUVHBMJEF-UHFFFAOYSA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.131

> <EXACT_MASS>
134.057908802

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.55105464816674

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3,4-trihydroxypentanal

> <ALOGPS_LOGP>
-1.74

> <JCHEM_LOGP>
-1.8911156543333332

> <ALOGPS_LOGS>
0.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.9123979936683

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.401243042355166

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0539920576398973

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
29.839399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.75e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3,4-trihydroxypentanal

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0246776 (5-Deoxy-D-ribose)

HMDB0246776
     RDKit          3D
5-Deoxy-D-ribose
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.3083   -0.0009    0.5222 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1240    0.0353   -0.4177 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0388    1.3403   -0.9276 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1134   -0.1964    0.3999 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1472   -1.4701    0.9655 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3873   -0.0451   -0.4079 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4603    1.1997   -1.0224 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5222   -0.2624    0.5129 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3735    0.5785    0.6659 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7554   -0.9994    0.6145 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0785    0.6721    0.0857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9989    0.4525    1.4799 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2891   -0.7162   -1.2070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6098    1.4646   -1.7255 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0988    0.5207    1.2417 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3098   -2.0745    0.3246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4351   -0.8179   -1.1961 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4000    1.5095   -0.9562 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5748   -1.1904    1.0474 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  4  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  3 14  1  0
  4 15  1  0
  5 16  1  0
  6 17  1  0
  7 18  1  0
  8 19  1  0
M  END
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PDB for HMDB0246776 (5-Deoxy-D-ribose)

HEADER    PROTEIN                                 11-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-21         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.976   3.644   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    4                                                            
CONECT    8    3                                                            
CONECT    9    2                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for HMDB0246776 (5-Deoxy-D-ribose)

COMPND    HMDB0246776
HETATM    1  C1  UNL     1      -2.308  -0.001   0.522  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.124   0.035  -0.418  1.00  0.00           C  
HETATM    3  O1  UNL     1      -1.039   1.340  -0.928  1.00  0.00           O  
HETATM    4  C3  UNL     1       0.113  -0.196   0.400  1.00  0.00           C  
HETATM    5  O2  UNL     1       0.147  -1.470   0.966  1.00  0.00           O  
HETATM    6  C4  UNL     1       1.387  -0.045  -0.408  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.460   1.200  -1.022  1.00  0.00           O  
HETATM    8  C5  UNL     1       2.522  -0.262   0.513  1.00  0.00           C  
HETATM    9  O4  UNL     1       3.374   0.578   0.666  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.755  -0.999   0.615  1.00  0.00           H  
HETATM   11  H2  UNL     1      -3.079   0.672   0.086  1.00  0.00           H  
HETATM   12  H3  UNL     1      -1.999   0.453   1.480  1.00  0.00           H  
HETATM   13  H4  UNL     1      -1.289  -0.716  -1.207  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.610   1.465  -1.725  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.099   0.521   1.242  1.00  0.00           H  
HETATM   16  H7  UNL     1      -0.310  -2.075   0.325  1.00  0.00           H  
HETATM   17  H8  UNL     1       1.435  -0.818  -1.196  1.00  0.00           H  
HETATM   18  H9  UNL     1       2.400   1.509  -0.956  1.00  0.00           H  
HETATM   19  H10 UNL     1       2.575  -1.190   1.047  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3    4   13
CONECT    3   14
CONECT    4    5    6   15
CONECT    5   16
CONECT    6    7    8   17
CONECT    7   18
CONECT    8    9    9   19
END
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SMILES for HMDB0246776 (5-Deoxy-D-ribose)

CC(O)C(O)C(O)C=O
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INCHI for HMDB0246776 (5-Deoxy-D-ribose)

InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC5H10O4
Average Molecular Weight134.131
Monoisotopic Molecular Weight134.057908802
IUPAC Name2,3,4-trihydroxypentanal
Traditional Name2,3,4-trihydroxypentanal
CAS Registry NumberNot Available
SMILES
CC(O)C(O)C(O)C=O
InChI Identifier
InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3
InChI KeyWDRISBUVHBMJEF-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentMonosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Beta-hydroxy aldehyde
  • Alpha-hydroxyaldehyde
  • Secondary alcohol
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Carbonyl group
  • Aldehyde
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
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
logP-1.7ALOGPS
logP-1.9ChemAxon
logS0.55ALOGPS
pKa (Strongest Acidic)12.4ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity29.84 m³·mol⁻¹ChemAxon
Polarizability12.55 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+126.9830932474
DeepCCS[M-H]-124.17930932474
DeepCCS[M-2H]-160.96430932474
DeepCCS[M+Na]+135.81730932474
AllCCS[M+H]+133.432859911
AllCCS[M+H-H2O]+129.332859911
AllCCS[M+NH4]+137.232859911
AllCCS[M+Na]+138.332859911
AllCCS[M-H]-124.532859911
AllCCS[M+Na-2H]-127.132859911
AllCCS[M+HCOO]-130.132859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.551 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20221.6 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid683.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid337.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid45.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid194.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid62.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid272.4 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 Acid240.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)239.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid606.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid53.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid811.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid192.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid243.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate563.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA327.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water301.3 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
5-Deoxy-D-riboseCC(O)C(O)C(O)C=O2627.5Standard polar33892256
5-Deoxy-D-riboseCC(O)C(O)C(O)C=O1105.4Standard non polar33892256
5-Deoxy-D-riboseCC(O)C(O)C(O)C=O1195.6Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
5-Deoxy-D-ribose,4TMS,isomer #1CC(O[Si](C)(C)C)C(O[Si](C)(C)C)C(=CO[Si](C)(C)C)O[Si](C)(C)C1577.4Semi standard non polar33892256
5-Deoxy-D-ribose,4TMS,isomer #1CC(O[Si](C)(C)C)C(O[Si](C)(C)C)C(=CO[Si](C)(C)C)O[Si](C)(C)C1512.6Standard non polar33892256
5-Deoxy-D-ribose,4TMS,isomer #1CC(O[Si](C)(C)C)C(O[Si](C)(C)C)C(=CO[Si](C)(C)C)O[Si](C)(C)C1477.6Standard polar33892256
5-Deoxy-D-ribose,4TBDMS,isomer #1CC(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2374.0Semi standard non polar33892256
5-Deoxy-D-ribose,4TBDMS,isomer #1CC(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2266.9Standard non polar33892256
5-Deoxy-D-ribose,4TBDMS,isomer #1CC(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)C(=CO[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C1985.3Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a70-9000000000-60141a80453b5d6a036b2021-09-23Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 5-Deoxy-D-ribose GC-MS (TBDMS_2_5) - 70eV, PositiveNot Available2021-11-03Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxy-D-ribose 10V, Positive-QTOFsplash10-000b-9100000000-d412d4ce233857a2b5b32021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxy-D-ribose 20V, Positive-QTOFsplash10-0002-9000000000-ffec40dec25b359642f52021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxy-D-ribose 40V, Positive-QTOFsplash10-0006-9000000000-a2e65202f2a39d91d7cf2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxy-D-ribose 10V, Negative-QTOFsplash10-00di-9400000000-4f712121612d7260318f2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxy-D-ribose 20V, Negative-QTOFsplash10-0006-9000000000-8871d3c4037ed2a096d72021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 5-Deoxy-D-ribose 40V, Negative-QTOFsplash10-0006-9000000000-80f423fe1924615d9baf2021-10-12Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-10-13Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID11384021
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound13420529
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. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Enzymes

Enzyme Details
1. 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
General function:
Not Available
Specific function:
Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Also cleaves 5'-deoxyadenosine, a toxic by-product of radical S-adenosylmethionine (SAM) enzymes, into 5-deoxyribose and adenine. Thus, is required for in vivo function of the radical SAM enzymes biotin synthase and lipoic acid synthase, that are inhibited by 5'-deoxyadenosine accumulation.
Gene Name:
MTNN
Uniprot ID:
Q5PD46
Molecular weight:
24373.725
Enzyme Details
2. 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
General function:
Not Available
Specific function:
Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Also cleaves 5'-deoxyadenosine, a toxic by-product of radical S-adenosylmethionine (SAM) enzymes, into 5-deoxyribose and adenine.
Gene Name:
MTNN
Uniprot ID:
Q4L6V0
Molecular weight:
24753.285
Enzyme Details
3. 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
General function:
Not Available
Specific function:
Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH/AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively. Also cleaves 5'-deoxyadenosine, a toxic by-product of radical S-adenosylmethionine (SAM) enzymes, into 5-deoxyribose and adenine. Thus, is required for in vivo function of the radical SAM enzymes biotin synthase and lipoic acid synthase, that are inhibited by 5'-deoxyadenosine accumulation.
Gene Name:
MTNN
Uniprot ID:
A1A7K5
Molecular weight:
24353.725
Enzyme Details
4. Aminodeoxyfutalosine nucleosidase
General function:
Not Available
Specific function:
Catalyzes the direct conversion of aminodeoxyfutalosine (AFL) into dehypoxanthine futalosine (DHFL) and adenine via the hydrolysis of the N-glycosidic bond; this reaction seems to represent an essential step in the menaquinone biosynthesis pathway in Helicobacter species. Also catalyzes the hydrolysis of 5'-methylthioadenosine (MTA) to adenine and 5'-methylthioribose. Can also probably use S-adenosylhomocysteine (SAH) as substrate, leading to adenine and S-ribosylhomocysteine. These other activities highlight the tremendous versatility of the enzyme, which also plays key roles in S-adenosylmethionine recycling and in the biosynthesis of the quorum-sensing molecule autoinducer-2.
Gene Name:
MTNN
Uniprot ID:
Q9ZMY2
Molecular weight:
25019.705