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Showing metabocard for 2-Deoxyribonic acid (HMDB0000366)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:14:45 UTC
HMDB IDHMDB0000366
Secondary Accession Numbers
  • HMDB00366
Metabolite Identification
Common Name2-Deoxyribonic acid
Description2-Deoxyribonic acid is the acid form of deoxyribonate (interconvertible with 2-Deoxyribonolactone), produced as part of bistranded lesions by DNA damaging agents, including the antitumor agents bleomycin and the neocarzinostatin chromophore (PMID 2523732 ). This lesion is also produced by ionizing radiation, organometallic oxidants, and is a metastable intermediate in DNA damage mediated by copper phenanthroline nucleases, and is also formed under anaerobic conditions in the presence of the radiosensitizing agent tirapazamine. (PMID 12600212 ), and it has been found in normal human biofluids (PMID 2925825 , 3829393 , 6725493 , 7228943 ).
Structure
Data?1676999685
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000366 (2-Deoxyribonic acid)


  Mrv0541 02231218292D          

 10  9  0  0  1  0            999 V2000
   16.0622  -12.4411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2056  -13.6786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9188  -13.6786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6333  -12.4411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0622  -13.2661    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.7767  -13.6786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.3478  -13.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4912  -13.2661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6333  -13.2661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7767  -14.5036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  6  0  0  0
  2  8  1  0  0  0  0
  3  9  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  6 10  1  1  0  0  0
M  END
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3D MOL for HMDB0000366 (2-Deoxyribonic acid)

HMDB0000366
     RDKit          3D
2-Deoxyribonic acid
 20 19  0  0  0  0  0  0  0  0999 V2000
    2.8986    0.2348    1.0617 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1425    0.3800    0.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1353    1.6068   -0.5676 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2926   -0.7281   -0.4325 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0765   -0.9292    0.4137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6609   -1.9899   -0.1154 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8342    0.2737    0.4459 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9091   -0.0532    1.2746 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4513    0.5521   -0.9111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3419    1.6133   -0.7620 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8143    2.3356   -0.4301 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8858   -1.6637   -0.3606 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0649   -0.5942   -1.5084 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4043   -1.1105    1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1530   -2.8185    0.1065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3529    1.1620    0.8767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1672   -0.9789    1.0386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7423    0.7615   -1.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0708   -0.3300   -1.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0310    2.2764   -0.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  1
  6 15  1  0
  7 16  1  1
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
M  END
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3D SDF for HMDB0000366 (2-Deoxyribonic acid)


  Mrv0541 02231218292D          

 10  9  0  0  1  0            999 V2000
   16.0622  -12.4411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.2056  -13.6786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9188  -13.6786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.6333  -12.4411    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0622  -13.2661    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.7767  -13.6786    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.3478  -13.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4912  -13.2661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6333  -13.2661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7767  -14.5036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  6  0  0  0
  2  8  1  0  0  0  0
  3  9  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  6 10  1  1  0  0  0
M  END
> <DATABASE_ID>
HMDB0000366

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@@H](O)[C@@H](O)CC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)/t3-,4+/m0/s1

> <INCHI_KEY>
VBUWJOHKCBQXNU-IUYQGCFVSA-N

> <FORMULA>
C5H10O5

> <MOLECULAR_WEIGHT>
150.1299

> <EXACT_MASS>
150.05282343

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
13.513982483742229

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4R)-3,4,5-trihydroxypentanoic acid

> <ALOGPS_LOGP>
-2.02

> <JCHEM_LOGP>
-2.064250908

> <ALOGPS_LOGS>
0.53

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.34947609043477

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.025609446634988

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9724107456054023

> <JCHEM_POLAR_SURFACE_AREA>
97.99

> <JCHEM_REFRACTIVITY>
30.970299999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S,4R)-3,4,5-trihydroxypentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0000366 (2-Deoxyribonic acid)

HMDB0000366
     RDKit          3D
2-Deoxyribonic acid
 20 19  0  0  0  0  0  0  0  0999 V2000
    2.8986    0.2348    1.0617 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1425    0.3800    0.0567 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1353    1.6068   -0.5676 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2926   -0.7281   -0.4325 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0765   -0.9292    0.4137 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6609   -1.9899   -0.1154 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8342    0.2737    0.4459 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9091   -0.0532    1.2746 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4513    0.5521   -0.9111 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3419    1.6133   -0.7620 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8143    2.3356   -0.4301 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8858   -1.6637   -0.3606 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0649   -0.5942   -1.5084 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4043   -1.1105    1.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1530   -2.8185    0.1065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3529    1.1620    0.8767 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1672   -0.9789    1.0386 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7423    0.7615   -1.7046 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0708   -0.3300   -1.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0310    2.2764   -0.0890 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  3 11  1  0
  4 12  1  0
  4 13  1  0
  5 14  1  1
  6 15  1  0
  7 16  1  1
  8 17  1  0
  9 18  1  0
  9 19  1  0
 10 20  1  0
M  END
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PDB for HMDB0000366 (2-Deoxyribonic acid)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  O   UNK     0      29.983 -23.223   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      33.984 -25.533   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      25.982 -25.533   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      27.315 -23.223   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      29.983 -24.763   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.317 -25.533   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      28.649 -25.533   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      32.650 -24.763   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      27.315 -24.763   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      31.317 -27.073   0.000  0.00  0.00           O+0
CONECT    1    5                                                            
CONECT    2    8                                                            
CONECT    3    9                                                            
CONECT    4    9                                                            
CONECT    5    1    6    7                                                  
CONECT    6    5    8   10                                                  
CONECT    7    5    9                                                       
CONECT    8    2    6                                                       
CONECT    9    3    4    7                                                  
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for HMDB0000366 (2-Deoxyribonic acid)

COMPND    HMDB0000366
HETATM    1  O1  UNL     1       2.899   0.235   1.062  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.143   0.380   0.057  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.135   1.607  -0.568  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.293  -0.728  -0.433  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.076  -0.929   0.414  1.00  0.00           C  
HETATM    6  O3  UNL     1      -0.661  -1.990  -0.115  1.00  0.00           O  
HETATM    7  C4  UNL     1      -0.834   0.274   0.446  1.00  0.00           C  
HETATM    8  O4  UNL     1      -1.909  -0.053   1.275  1.00  0.00           O  
HETATM    9  C5  UNL     1      -1.451   0.552  -0.911  1.00  0.00           C  
HETATM   10  O5  UNL     1      -2.342   1.613  -0.762  1.00  0.00           O  
HETATM   11  H1  UNL     1       2.814   2.336  -0.430  1.00  0.00           H  
HETATM   12  H2  UNL     1       1.886  -1.664  -0.361  1.00  0.00           H  
HETATM   13  H3  UNL     1       1.065  -0.594  -1.508  1.00  0.00           H  
HETATM   14  H4  UNL     1       0.404  -1.110   1.444  1.00  0.00           H  
HETATM   15  H5  UNL     1      -0.153  -2.818   0.106  1.00  0.00           H  
HETATM   16  H6  UNL     1      -0.353   1.162   0.877  1.00  0.00           H  
HETATM   17  H7  UNL     1      -2.167  -0.979   1.039  1.00  0.00           H  
HETATM   18  H8  UNL     1      -0.742   0.762  -1.705  1.00  0.00           H  
HETATM   19  H9  UNL     1      -2.071  -0.330  -1.230  1.00  0.00           H  
HETATM   20  H10 UNL     1      -2.031   2.276  -0.089  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5   12   13
CONECT    5    6    7   14
CONECT    6   15
CONECT    7    8    9   16
CONECT    8   17
CONECT    9   10   18   19
CONECT   10   20
END
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SMILES for HMDB0000366 (2-Deoxyribonic acid)

OC[C@@H](O)[C@@H](O)CC(O)=O
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INCHI for HMDB0000366 (2-Deoxyribonic acid)

InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)/t3-,4+/m0/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
2-DeoxyribonateGenerator
2-Deoxy-D-ribonateHMDB
2-Deoxy-D-ribonic acidHMDB
Chemical FormulaC5H10O5
Average Molecular Weight150.1299
Monoisotopic Molecular Weight150.05282343
IUPAC Name(3S,4R)-3,4,5-trihydroxypentanoic acid
Traditional Name(3S,4R)-3,4,5-trihydroxypentanoic acid
CAS Registry Number29625-75-0
SMILES
OC[C@@H](O)[C@@H](O)CC(O)=O
InChI Identifier
InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)/t3-,4+/m0/s1
InChI KeyVBUWJOHKCBQXNU-IUYQGCFVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassHydroxy acids and derivatives
Sub ClassBeta hydroxy acids and derivatives
Direct ParentBeta hydroxy acids and derivatives
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Short-chain hydroxy acid
  • Fatty acid
  • Secondary alcohol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Polyol
  • Organooxygen compound
  • Organic oxygen compound
  • Alcohol
  • Carbonyl group
  • Primary alcohol
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
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 Solubility511 g/LALOGPS
logP-2ALOGPS
logP-2.1ChemAxon
logS0.53ALOGPS
pKa (Strongest Acidic)4.03ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity30.97 m³·mol⁻¹ChemAxon
Polarizability13.51 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
DarkChem[M+H]+132.131661259
DarkChem[M-H]-125.72631661259
AllCCS[M+H]+135.25932859911
AllCCS[M-H]-127.29432859911
DeepCCS[M+H]+131.94930932474
DeepCCS[M-H]-128.61530932474
DeepCCS[M-2H]-165.66730932474
DeepCCS[M+Na]+141.20530932474
AllCCS[M+H]+135.332859911
AllCCS[M+H-H2O]+131.332859911
AllCCS[M+NH4]+139.032859911
AllCCS[M+Na]+140.032859911
AllCCS[M-H]-127.332859911
AllCCS[M+Na-2H]-129.532859911
AllCCS[M+HCOO]-132.032859911

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, 2022.1.37 minutes32390414
Predicted by Siyang on May 30, 20229.5949 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20225.73 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid328.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid626.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid325.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid35.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid194.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid70.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid288.8 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 Acid230.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)663.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid588.9 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid39.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid813.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid200.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid262.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate638.2 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA331.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water371.4 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2-Deoxyribonic acidOC[C@@H](O)[C@@H](O)CC(O)=O2819.1Standard polar33892256
2-Deoxyribonic acidOC[C@@H](O)[C@@H](O)CC(O)=O1448.2Standard non polar33892256
2-Deoxyribonic acidOC[C@@H](O)[C@@H](O)CC(O)=O1478.1Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
2-Deoxyribonic acid,1TMS,isomer #1C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)O1459.5Semi standard non polar33892256
2-Deoxyribonic acid,1TMS,isomer #2C[Si](C)(C)O[C@H](CO)[C@@H](O)CC(=O)O1463.1Semi standard non polar33892256
2-Deoxyribonic acid,1TMS,isomer #3C[Si](C)(C)O[C@@H](CC(=O)O)[C@H](O)CO1468.7Semi standard non polar33892256
2-Deoxyribonic acid,1TMS,isomer #4C[Si](C)(C)OC(=O)C[C@H](O)[C@H](O)CO1491.5Semi standard non polar33892256
2-Deoxyribonic acid,2TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC(=O)O1543.8Semi standard non polar33892256
2-Deoxyribonic acid,2TMS,isomer #2C[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)O)O[Si](C)(C)C1541.5Semi standard non polar33892256
2-Deoxyribonic acid,2TMS,isomer #3C[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)O[Si](C)(C)C1569.0Semi standard non polar33892256
2-Deoxyribonic acid,2TMS,isomer #4C[Si](C)(C)O[C@@H](CC(=O)O)[C@@H](CO)O[Si](C)(C)C1539.5Semi standard non polar33892256
2-Deoxyribonic acid,2TMS,isomer #5C[Si](C)(C)OC(=O)C[C@H](O)[C@@H](CO)O[Si](C)(C)C1546.5Semi standard non polar33892256
2-Deoxyribonic acid,2TMS,isomer #6C[Si](C)(C)OC(=O)C[C@H](O[Si](C)(C)C)[C@H](O)CO1538.5Semi standard non polar33892256
2-Deoxyribonic acid,3TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC(=O)O)O[Si](C)(C)C1629.7Semi standard non polar33892256
2-Deoxyribonic acid,3TMS,isomer #2C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@@H](O)CC(=O)O[Si](C)(C)C1635.6Semi standard non polar33892256
2-Deoxyribonic acid,3TMS,isomer #3C[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1624.7Semi standard non polar33892256
2-Deoxyribonic acid,3TMS,isomer #4C[Si](C)(C)OC(=O)C[C@H](O[Si](C)(C)C)[C@@H](CO)O[Si](C)(C)C1612.8Semi standard non polar33892256
2-Deoxyribonic acid,4TMS,isomer #1C[Si](C)(C)OC[C@@H](O[Si](C)(C)C)[C@H](CC(=O)O[Si](C)(C)C)O[Si](C)(C)C1684.1Semi standard non polar33892256
2-Deoxyribonic acid,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)O1751.2Semi standard non polar33892256
2-Deoxyribonic acid,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@H](CO)[C@@H](O)CC(=O)O1735.0Semi standard non polar33892256
2-Deoxyribonic acid,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@@H](CC(=O)O)[C@H](O)CO1726.0Semi standard non polar33892256
2-Deoxyribonic acid,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O)[C@H](O)CO1723.7Semi standard non polar33892256
2-Deoxyribonic acid,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O)CC(=O)O2028.6Semi standard non polar33892256
2-Deoxyribonic acid,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)O)O[Si](C)(C)C(C)(C)C2010.7Semi standard non polar33892256
2-Deoxyribonic acid,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@@H](O)CC(=O)O[Si](C)(C)C(C)(C)C1999.0Semi standard non polar33892256
2-Deoxyribonic acid,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H](CC(=O)O)[C@@H](CO)O[Si](C)(C)C(C)(C)C2021.0Semi standard non polar33892256
2-Deoxyribonic acid,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O)[C@@H](CO)O[Si](C)(C)C(C)(C)C2002.5Semi standard non polar33892256
2-Deoxyribonic acid,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CO1976.0Semi standard non polar33892256
2-Deoxyribonic acid,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CC(=O)O)O[Si](C)(C)C(C)(C)C2285.6Semi standard non polar33892256
2-Deoxyribonic acid,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H](O)CC(=O)O[Si](C)(C)C(C)(C)C2291.6Semi standard non polar33892256
2-Deoxyribonic acid,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H](O)[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2280.3Semi standard non polar33892256
2-Deoxyribonic acid,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)OC(=O)C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](CO)O[Si](C)(C)C(C)(C)C2288.5Semi standard non polar33892256
2-Deoxyribonic acid,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CC(=O)O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C2505.9Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (Non-derivatized) - 70eV, Positivesplash10-06sc-9000000000-c78de6841f3acf1fa76b2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (4 TMS) - 70eV, Positivesplash10-00g0-9027200000-adc32665fe9b412fb0fb2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_1_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_2_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_2_5) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_2_6) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_3_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_3_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_3_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TMS_3_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_1_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_1_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_1_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_2_1) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_2_2) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_2_3) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2-Deoxyribonic acid GC-MS (TBDMS_2_4) - 70eV, PositiveNot Available2021-11-05Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 10V, Positive-QTOFsplash10-001i-1900000000-abab4e4ee07915ad25df2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 20V, Positive-QTOFsplash10-07cu-9700000000-56ec7d5976e9023705802017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 40V, Positive-QTOFsplash10-06xx-9000000000-cb82a1f13b50d91492bd2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 10V, Negative-QTOFsplash10-052b-3900000000-0b54ad95ab8a0e82a5a02017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 20V, Negative-QTOFsplash10-0a4r-9300000000-1190b2589b795883f41c2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 40V, Negative-QTOFsplash10-0a4l-9000000000-6a9184456a482fb916e12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 10V, Negative-QTOFsplash10-0a4j-3900000000-a9aa746c80102cdac1262021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 20V, Negative-QTOFsplash10-0a4l-9000000000-9dafbd8baf4cb85faab22021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 40V, Negative-QTOFsplash10-0006-9000000000-01325c407d88a7a206322021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 10V, Positive-QTOFsplash10-00li-7900000000-a34eed2d06f591b7cbbd2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 20V, Positive-QTOFsplash10-00xv-9300000000-8da3691bcbc57bad1a6c2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2-Deoxyribonic acid 40V, Positive-QTOFsplash10-0006-9000000000-7a979d2ff58310d5e57c2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-16Wishart LabView Spectrum

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-03FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-03FELIX labView Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021985
KNApSAcK IDNot Available
Chemspider ID9703151
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5355
PubChem Compound11528367
PDB IDNot Available
ChEBI ID86350
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceYang, Byung Yun; Montgomery, Rex. Alkaline degradation of fructofuranosides. Carbohydrate Research (1996), 280(1), 47-57.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Davies M, Adams PH, Berry JL, Lumb GA, Klimiuk PS, Mawer EB, Wain D: Familial hypocalciuric hypercalcaemia: observations on vitamin D metabolism and parathyroid function. Acta Endocrinol (Copenh). 1983 Oct;104(2):210-5. [PubMed:6314724 ]
  2. Lefevere MF, Verhaeghe BJ, Declerck DH, Van Bocxlaer JF, De Leenheer AP, De Sagher RM: Metabolic profiling of urinary organic acids by single and multicolumn capillary gas chromatography. J Chromatogr Sci. 1989 Jan;27(1):23-9. [PubMed:2925825 ]
  3. Chamberlin BA, Sweeley CC: Metabolic profiles of urinary organic acids recovered from absorbent filter paper. Clin Chem. 1987 Apr;33(4):572-6. [PubMed:3829393 ]
  4. Kappen LS, Goldberg IH: Identification of 2-deoxyribonolactone at the site of neocarzinostatin-induced cytosine release in the sequence d(AGC). Biochemistry. 1989 Feb 7;28(3):1027-32. [PubMed:2523732 ]
  5. Kroeger KM, Hashimoto M, Kow YW, Greenberg MM: Cross-linking of 2-deoxyribonolactone and its beta-elimination product by base excision repair enzymes. Biochemistry. 2003 Mar 4;42(8):2449-55. [PubMed:12600212 ]
  6. Tuchman M, Bowers LD, Fregien KD, Crippin PJ, Krivit W: Capillary gas chromatographic separation of urinary organic acids. Retention indices of 101 urinary acids on a 5% phenylmethyl silicone capillary column. J Chromatogr Sci. 1984 May;22(5):198-202. [PubMed:6725493 ]
  7. Sims P, Truscott R, Halpern B: Improved procedure for the anion-exchange isolation of urinary organic acids. J Chromatogr. 1981 Mar 13;222(3):337-44. [PubMed:7228943 ]