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Showing NP-Card for 2-Deoxyribonic acid (NP0086561)

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Record Information
Version2.0
Created at2022-05-11 16:24:28 UTC
Updated at2022-05-11 16:24:28 UTC
NP-MRD IDNP0086561
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Deoxyribonic acid
Description2-Deoxyribonic acid, also known as 2-deoxyribonate, 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. 2-Deoxyribonic acid was first documented in 1989 (PMID: 2523732). 2-Deoxyribonic acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086561 (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
Download

3D MOL for NP0086561 (2-Deoxyribonic acid)

     RDKit          3D

 20 19  0  0  0  0  0  0  0  0999 V2000
    1.7322   -1.2782    1.5428 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1469   -0.5489    0.6050 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2374    0.2671    0.8710 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4570   -0.6048   -0.7049 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1449    0.1488   -0.6880 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3398    1.4968   -0.5814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8093   -0.4137    0.3358 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9547   -1.7884    0.1633 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1656    0.2063    0.2701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0718    1.6032    0.4404 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3428    1.1773    0.4432 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3041   -1.6565   -1.0479 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1039   -0.0713   -1.4520 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3280   -0.0423   -1.6935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3140    2.0572   -1.0307 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3674   -0.2681    1.3394 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5764   -1.9139   -0.6049 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7755   -0.1530    1.1193 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7173   -0.0499   -0.6468 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7290    1.8324    1.3200 H   0  0  0  0  0  0  0  0  0  0  0  0
 10  9  1  0
  9  7  1  0
  7  8  1  0
  7  5  1  0
  5  6  1  0
  5  4  1  0
  4  2  1  0
  2  3  1  0
  2  1  2  0
 10 20  1  0
  9 18  1  0
  9 19  1  0
  7 16  1  1
  8 17  1  0
  5 14  1  6
  6 15  1  0
  4 12  1  0
  4 13  1  0
  3 11  1  0
M  END
Download

3D SDF for NP0086561 (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>
NP0086561

> <DATABASE_NAME>
NP-MRD

> <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

$$$$
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3D-SDF for NP0086561 (2-Deoxyribonic acid)

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PDB for NP0086561 (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 NP0086561 (2-Deoxyribonic acid)
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SMILES for NP0086561 (2-Deoxyribonic acid)
OC[C@@H](O)[C@@H](O)CC(O)=O
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INCHI for NP0086561 (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 JSmol
Synonyms
ValueSource
2-DeoxyribonateGenerator
2-Deoxy-D-ribonateHMDB
2-Deoxy-D-ribonic acidHMDB
Chemical FormulaC5H10O5
Average Mass150.1299 Da
Monoisotopic Mass150.05282 Da
IUPAC Name(3S,4R)-3,4,5-trihydroxypentanoic acid
Traditional Name(3S,4R)-3,4,5-trihydroxypentanoic acid
CAS Registry NumberNot Available
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
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchosFooDB
AnatidaeFooDB
Anser anserFooDB
Bison bisonFooDB
Bos taurusFooDB
Bos taurus X Bison bisonFooDB
Bubalus bubalisFooDB
Capra aegagrus hircusFooDB
CervidaeFooDB
Cervus canadensisFooDB
ColumbaFooDB
ColumbidaeFooDB
Dromaius novaehollandiaeFooDB
Equus caballusFooDB
Gallus gallusFooDB
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Numida meleagrisFooDB
OdocoileusFooDB
OryctolagusFooDB
Ovis ariesFooDB
PhasianidaeFooDB
Phasianus colchicusFooDB
Struthio camelusFooDB
Sus scrofaFooDB
Sus scrofa domesticaFooDB
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
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
HMDB IDHMDB0000366  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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  
Good Scents IDNot Available
References
General References
  1. 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. doi: 10.1021/bi00429a016. [PubMed:2523732  ]