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Showing NP-Card for 3-Hydroxyvaleric acid (NP0086605)

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Record Information
Version2.0
Created at2022-05-11 16:25:49 UTC
Updated at2022-05-11 16:25:49 UTC
NP-MRD IDNP0086605
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Hydroxyvaleric acid
Description3-Hydroxyvaleric acid, also known as 3-hydroxy valerate or 3-hydroxy-pentanoic acid, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 3-Hydroxyvaleric acid is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. In humans, 3-hydroxyvaleric acid is involved in the metabolic disorder called methylmalonic aciduria due to cobalamin-related disorders. 3-Hydroxyvaleric acid is a potentially toxic compound. 3-Hydroxyvaleric acid was first documented in 1978 (PMID: 630060). 3-Hydroxyvaleric acid, with regard to humans, has been linked to the inborn metabolic disorder propionic acidemia (PMID: 6111361) (PMID: 6200156) (PMID: 3906131) (PMID: 1831712).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0086605 (3-Hydroxyvaleric acid)

3-Hydroxyvaleric acid.mol
  Mrv0541 02231218342D          

  8  7  0  0  0  0            999 V2000
    0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    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
M  END
Download

3D MOL for NP0086605 (3-Hydroxyvaleric acid)

     RDKit          3D

 18 17  0  0  0  0  0  0  0  0999 V2000
   -2.2892    0.6980    0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8726    0.5473    0.5033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1943   -0.5978   -0.1932 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9050   -1.7790    0.0686 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2104   -0.8128    0.2583 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0675    0.3649    0.0236 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9270    1.4504    0.6665 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0777    0.3420   -0.9216 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4423   -0.0270   -0.8136 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0150    0.4904    0.8372 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4852    1.7437   -0.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9216    0.4157    1.6021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3387    1.4913    0.2912 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1858   -0.4104   -1.2740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3011   -2.1376   -0.7418 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2370   -1.1064    1.3417 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6193   -1.6694   -0.3262 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8120    0.9965   -1.0019 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
  6  8  1  0
  6  7  2  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  2 13  1  0
  3 14  1  6
  4 15  1  0
  5 16  1  0
  5 17  1  0
  8 18  1  0
M  END
Download

3D SDF for NP0086605 (3-Hydroxyvaleric acid)

3-Hydroxyvaleric acid.mol
  Mrv0541 02231218342D          

  8  7  0  0  0  0            999 V2000
    0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    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
M  END
> <DATABASE_ID>
NP0086605

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O3/c1-2-4(6)3-5(7)8/h4,6H,2-3H2,1H3,(H,7,8)

> <INCHI_KEY>
REKYPYSUBKSCAT-UHFFFAOYSA-N

> <FORMULA>
C5H10O3

> <MOLECULAR_WEIGHT>
118.1311

> <EXACT_MASS>
118.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
11.951656326084933

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxypentanoic acid

> <ALOGPS_LOGP>
0.04

> <JCHEM_LOGP>
0.13551639566666668

> <ALOGPS_LOGS>
0.50

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.297523317831931

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.558402482827193

> <JCHEM_PKA_STRONGEST_BASIC>
-2.7946405200846556

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
27.988100000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.71e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
β-hydroxyvaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0086605 (3-Hydroxyvaleric acid)

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PDB for NP0086605 (3-Hydroxyvaleric acid)
HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Hydroxyvaleric acid.mol                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -1.925   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.334   1.925   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       2.667  -0.385   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -1.334   1.925   0.000  0.00  0.00           O+0
CONECT    1    2    6    7                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    3                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0086605 (3-Hydroxyvaleric acid)
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SMILES for NP0086605 (3-Hydroxyvaleric acid)
CCC(O)CC(O)=O
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INCHI for NP0086605 (3-Hydroxyvaleric acid)
InChI=1S/C5H10O3/c1-2-4(6)3-5(7)8/h4,6H,2-3H2,1H3,(H,7,8)
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View in JSmol
Synonyms
ValueSource
3-Hydroxy valeric acidChEBI
3-Hydroxy-pentanoic acidChEBI
3-Hydroxy-valeric acidChEBI
beta-Hydroxypentanoic acidChEBI
beta-Hydroxyvaleric acidChEBI
3-Hydroxy valerateGenerator
3-Hydroxy-pentanoateGenerator
3-Hydroxy-valerateGenerator
b-HydroxypentanoateGenerator
b-Hydroxypentanoic acidGenerator
beta-HydroxypentanoateGenerator
Β-hydroxypentanoateGenerator
Β-hydroxypentanoic acidGenerator
b-HydroxyvalerateGenerator
b-Hydroxyvaleric acidGenerator
beta-HydroxyvalerateGenerator
Β-hydroxyvalerateGenerator
Β-hydroxyvaleric acidGenerator
3-HydroxyvalerateGenerator
3-Hydroxy-N-valerateHMDB
3-Hydroxy-N-valeric acidHMDB
3-HydroxypentanoateHMDB
3-Hydroxypentanoic acidHMDB
b-Hydroxy-N-valerateHMDB
b-Hydroxy-N-valeric acidHMDB
beta-Hydroxy-N-valerateHMDB
beta-Hydroxy-N-valeric acidHMDB
3-Hydroxyvaleric acidChEBI
Chemical FormulaC5H10O3
Average Mass118.1311 Da
Monoisotopic Mass118.06299 Da
IUPAC Name3-hydroxypentanoic acid
Traditional Nameβ-hydroxyvaleric acid
CAS Registry NumberNot Available
SMILES
CCC(O)CC(O)=O
InChI Identifier
InChI=1S/C5H10O3/c1-2-4(6)3-5(7)8/h4,6H,2-3H2,1H3,(H,7,8)
InChI KeyREKYPYSUBKSCAT-UHFFFAOYSA-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 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
    • 

  • Hydroxy acid
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Organooxygen compound
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • 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
logP0.04ALOGPS
logP0.14ChemAxon
logS0.5ALOGPS
pKa (Strongest Acidic)4.56ChemAxon
pKa (Strongest Basic)-2.8ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity27.99 m³·mol⁻¹ChemAxon
Polarizability11.95 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000531  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022099  
KNApSAcK IDNot Available
Chemspider ID96952  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia Link3-Hydroxypentanoic_acid  
METLIN ID5516  
PubChem Compound107802  
PDB IDNot Available
ChEBI ID139272  
Good Scents IDNot Available
References
General References
  1. Kuhara T, Matsumoto I: Studies on the urinary acidic metabolites from three patients with methylmalonic aciduria. Biomed Mass Spectrom. 1980 Oct;7(10):424-8. [PubMed:6111361  ] 
  2. Sweetman L, Weyler W, Nyhan WL, de Cespedes C, Loria AR, Estrada Y: Abnormal metabolites of isoleucine in a patient with propionyl-CoA carboxylase deficiency. Biomed Mass Spectrom. 1978 Mar;5(3):198-207. [PubMed:630060  ] 
  3. Kuhara T, Inoue Y, Shinka T, Matsumoto I, Matsuo M: Identification of 3-hydroxy-3-ethylglutaric acid in urine of patients with propionic acidaemia. Biomed Mass Spectrom. 1983 Dec;10(12):629-32. doi: 10.1002/bms.1200101202. [PubMed:6200156  ] 
  4. Boger J, Payne LS, Perlow DS, Lohr NS, Poe M, Blaine EH, Ulm EH, Schorn TW, LaMont BI, Lin TY, et al.: Renin inhibitors. Syntheses of subnanomolar, competitive, transition-state analogue inhibitors containing a novel analogue of statine. J Med Chem. 1985 Dec;28(12):1779-90. doi: 10.1021/jm00150a007. [PubMed:3906131  ] 
  5. Yuan L: [Propionic acidemia: one case report]. Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 1991 Apr;13(2):141-3. [PubMed:1831712  ]