Np mrd loader

Showing NP-Card for 2,3-Dihydroxyvaleric acid (NP0000311)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2021-08-09 22:32:59 UTC
NP-MRD IDNP0000311
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3-Dihydroxyvaleric acid
Description2,3-Dihydroxyvaleric acid (DHVA) belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. This compound has been detected in extracts from the purple carrot (https://Doi.Org/10.3390/App10238493). It is likely a hydroxylation derivative of the more common 2-hydroxyvaleric acid (an algal metabolite derived from a valeric acid) or 3-hydroxyvaleric acid (a 5-carbon ketone body made from odd carbon fatty acids in the liver). Very little is known about the origin of this particular hydroxy fatty acid.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000311 (2,3-Dihydroxyvaleric acid)

2,3-dihydroxy-Valeric acid.mol
  Mrv1652305261923552D          

  9  8  0  0  0  0            999 V2000
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    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
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  3  8  1  0  0  0  0
  2  9  1  0  0  0  0
M  END
Download

3D MOL for NP0000311 (2,3-Dihydroxyvaleric acid)

HMDB0000421
     RDKit          3D
2,3-Dihydroxyvaleric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.1987    0.6634    0.8784 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765    0.4879    0.9959 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3055   -0.4759   -0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6426    0.0104   -1.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1380   -0.8706   -0.1084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911   -1.8591   -1.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0654    0.2169   -0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8200    0.1762   -1.4175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1049    1.3409    0.4160 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6958   -0.2445    1.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4113    0.7290   -0.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5419    1.5712    1.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5179    0.0318    1.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1633    1.4435    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9001   -1.4032    0.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4636   -0.4103   -1.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4341   -1.3636    0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7040   -1.7331   -1.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9597    1.6891    0.8112 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  9 19  1  0
M  END
Download

3D SDF for NP0000311 (2,3-Dihydroxyvaleric acid)

2,3-dihydroxy-Valeric acid.mol
  Mrv1652305261923552D          

  9  8  0  0  0  0            999 V2000
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7862    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7862   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    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
  1  6  2  0  0  0  0
  1  7  1  0  0  0  0
  3  8  1  0  0  0  0
  2  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000311

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c1-2-3(6)4(7)5(8)9/h3-4,6-7H,2H2,1H3,(H,8,9)

> <INCHI_KEY>
CJXCLBPFKGZXJP-UHFFFAOYSA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.1305

> <EXACT_MASS>
134.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.717206006383734

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxypentanoic acid

> <ALOGPS_LOGP>
-0.87

> <JCHEM_LOGP>
-0.579642065

> <ALOGPS_LOGS>
0.42

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.264842121326641

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.8016080976510094

> <JCHEM_PKA_STRONGEST_BASIC>
-3.254534149492307

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
29.326299999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxyvaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0000311 (2,3-Dihydroxyvaleric acid)

HMDB0000421
     RDKit          3D
2,3-Dihydroxyvaleric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.1987    0.6634    0.8784 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6765    0.4879    0.9959 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3055   -0.4759   -0.1005 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6426    0.0104   -1.3592 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1380   -0.8706   -0.1084 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2911   -1.8591   -1.0810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0654    0.2169   -0.4254 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8200    0.1762   -1.4175 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1049    1.3409    0.4160 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6958   -0.2445    1.2558 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4113    0.7290   -0.2027 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5419    1.5712    1.3793 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5179    0.0318    1.9942 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1633    1.4435    0.9596 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9001   -1.4032    0.0673 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4636   -0.4103   -1.6924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4341   -1.3636    0.8607 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7040   -1.7331   -1.8610 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9597    1.6891    0.8112 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  3  5  1  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  6 18  1  0
  9 19  1  0
M  END
Download

PDB for NP0000311 (2,3-Dihydroxyvaleric acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 2,3-dihydroxy-Valeric acid.mol                    
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         0                                  
HETATM    1  C   UNK     0       2.001   0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.667  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.667   0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.001  -0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.334   0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       2.001   1.925   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       3.334  -0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.667   1.925   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.667  -1.925   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3    9                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    3                                                            
CONECT    9    2                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
Download

3D PDB for NP0000311 (2,3-Dihydroxyvaleric acid)

COMPND    HMDB0000421
HETATM    1  C1  UNL     1       2.199   0.663   0.878  1.00  0.00           C  
HETATM    2  C2  UNL     1       0.677   0.488   0.996  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.305  -0.476  -0.100  1.00  0.00           C  
HETATM    4  O1  UNL     1       0.643   0.010  -1.359  1.00  0.00           O  
HETATM    5  C4  UNL     1      -1.138  -0.871  -0.108  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.291  -1.859  -1.081  1.00  0.00           O  
HETATM    7  C5  UNL     1      -2.065   0.217  -0.425  1.00  0.00           C  
HETATM    8  O3  UNL     1      -2.820   0.176  -1.417  1.00  0.00           O  
HETATM    9  O4  UNL     1      -2.105   1.341   0.416  1.00  0.00           O  
HETATM   10  H1  UNL     1       2.696  -0.245   1.256  1.00  0.00           H  
HETATM   11  H2  UNL     1       2.411   0.729  -0.203  1.00  0.00           H  
HETATM   12  H3  UNL     1       2.542   1.571   1.379  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.518   0.032   1.994  1.00  0.00           H  
HETATM   14  H5  UNL     1       0.163   1.443   0.960  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.900  -1.403   0.067  1.00  0.00           H  
HETATM   16  H7  UNL     1       1.464  -0.410  -1.692  1.00  0.00           H  
HETATM   17  H8  UNL     1      -1.434  -1.364   0.861  1.00  0.00           H  
HETATM   18  H9  UNL     1      -0.704  -1.733  -1.861  1.00  0.00           H  
HETATM   19  H10 UNL     1      -2.960   1.689   0.811  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4    5   15
CONECT    4   16
CONECT    5    6    7   17
CONECT    6   18
CONECT    7    8    8    9
CONECT    9   19
END
Download

SMILES for NP0000311 (2,3-Dihydroxyvaleric acid)

CCC(O)C(O)C(O)=O
Download

INCHI for NP0000311 (2,3-Dihydroxyvaleric acid)

InChI=1S/C5H10O4/c1-2-3(6)4(7)5(8)9/h3-4,6-7H,2H2,1H3,(H,8,9)
Download
View in JSmol
Synonyms
ValueSource
2,3-DihydroxyvalerateGenerator
2,3-Dihydroxy-valerateHMDB
2,3-Dihydroxy-valeric acidHMDB
Chemical FormulaC5H10O4
Average Mass134.1305 Da
Monoisotopic Mass134.05791 Da
IUPAC Name2,3-dihydroxypentanoic acid
Traditional Name2,3-dihydroxyvaleric acid
CAS Registry Number26386-47-0
SMILES
CCC(O)C(O)C(O)=O
InChI Identifier
InChI=1S/C5H10O4/c1-2-3(6)4(7)5(8)9/h3-4,6-7H,2H2,1H3,(H,8,9)
InChI KeyCJXCLBPFKGZXJP-UHFFFAOYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, simulated)varshavi.d26@gmail.comNot AvailableNot Available2021-08-11View Spectrum
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 hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acids and conjugates
Direct ParentHydroxy fatty acids
Alternative Parents
Substituents
  • Beta-hydroxy acid
  • Branched fatty acid
  • Hydroxy fatty acid
  • Short-chain hydroxy acid
  • Methyl-branched fatty acid
  • Monosaccharide
  • Hydroxy acid
  • Alpha-hydroxy acid
  • Secondary alcohol
  • 1,2-diol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility349 g/LALOGPS
logP-0.87ALOGPS
logP-0.58ChemAxon
logS0.42ALOGPS
pKa (Strongest Acidic)3.8ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity29.33 m³·mol⁻¹ChemAxon
Polarizability12.72 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000421
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022035
KNApSAcK IDNot Available
Chemspider ID13451358
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5410
PubChem Compound20848966
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Holmes E, Foxall PJ, Spraul M, Farrant RD, Nicholson JK, Lindon JC: 750 MHz 1H NMR spectroscopy characterisation of the complex metabolic pattern of urine from patients with inborn errors of metabolism: 2-hydroxyglutaric aciduria and maple syrup urine disease. J Pharm Biomed Anal. 1997 Jul;15(11):1647-59. [PubMed:9260660 ]