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Showing NP-Card for 2-Hydroxy-3-methylpentanoic acid (NP0083428)

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Record Information
Version1.0
Created at2022-04-29 04:28:45 UTC
Updated at2022-04-29 04:28:45 UTC
NP-MRD IDNP0083428
Secondary Accession NumbersNone
Natural Product Identification
Common Name2-Hydroxy-3-methylpentanoic acid
Description2-Hydroxy-3-methylpentanoic acid, also known as alpha-hydroxy-beta-methylvaleric acid or isoleucic 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. 2-Hydroxy-3-methylpentanoic acid is found in Homo sapiens (Urine) and Nicotiana tabacum. 2-Hydroxy-3-methylpentanoic acid is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0083428 (2-Hydroxy-3-methylpentanoic acid)


  Mrv1533004191517052D          

  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
    1.2375   -0.1105    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
    1.9520    1.9520    0.0000 O   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
    2.6664   -0.1105    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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
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3D MOL for NP0083428 (2-Hydroxy-3-methylpentanoic acid)

     RDKit          3D

 21 20  0  0  0  0  0  0  0  0999 V2000
   -2.1085    1.0519    0.4054 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6599    0.7118    0.7826 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1391   -0.1575   -0.3182 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0490   -1.3940   -0.3516 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2525   -0.6904   -0.0971 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5325   -1.4732   -1.2447 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2757    0.3633    0.0739 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2135    0.4714   -0.7505 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1779    1.2125    1.1446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8086    0.4462    1.0124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2654    2.1551    0.5616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3127    0.8495   -0.6566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6309    0.1609    1.7445 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0938    1.6577    0.9204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1608    0.3579   -1.2951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4917   -2.1472   -0.9779 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1417   -1.7303    0.6905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9871   -1.1872   -0.8619 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2318   -1.3942    0.7706 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2344   -0.8968   -2.0066 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9308    1.6327    1.6389 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  9  1  0
  7  8  2  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  6
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  1
  6 20  1  0
  9 21  1  0
M  END
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3D SDF for NP0083428 (2-Hydroxy-3-methylpentanoic acid)


  Mrv1533004191517052D          

  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
    1.2375   -0.1105    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
    1.9520    1.9520    0.0000 O   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
    2.6664   -0.1105    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
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0083428

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)

> <INCHI_KEY>
RILPIWOPNGRASR-UHFFFAOYSA-N

> <FORMULA>
C6H12O3

> <MOLECULAR_WEIGHT>
132.159

> <EXACT_MASS>
132.078644246

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
13.7091304513666

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-hydroxy-3-methylpentanoic acid

> <ALOGPS_LOGP>
0.74

> <JCHEM_LOGP>
0.8602343683333333

> <ALOGPS_LOGS>
0.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.044948135264622

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.25405925572059

> <JCHEM_PKA_STRONGEST_BASIC>
-3.8957913795351873

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
32.436400000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.49e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxy-3-methylvaleric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0083428 (2-Hydroxy-3-methylpentanoic acid)

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PDB for NP0083428 (2-Hydroxy-3-methylpentanoic acid)
HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         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       2.310  -0.206   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0083428 (2-Hydroxy-3-methylpentanoic acid)
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SMILES for NP0083428 (2-Hydroxy-3-methylpentanoic acid)
CCC(C)C(O)C(O)=O
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INCHI for NP0083428 (2-Hydroxy-3-methylpentanoic acid)
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)
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View in JSmol
Synonyms
ValueSource
2-Hydroxy-3-methylvaleric acidChEBI
alpha-Hydroxy-beta-methylpentanoic acidChEBI
alpha-Hydroxy-beta-methylvaleric acidChEBI
Isoleucic acidChEBI
2-Hydroxy-3-methylvalerateGenerator
a-Hydroxy-b-methylpentanoateGenerator
a-Hydroxy-b-methylpentanoic acidGenerator
alpha-Hydroxy-beta-methylpentanoateGenerator
Α-hydroxy-β-methylpentanoateGenerator
Α-hydroxy-β-methylpentanoic acidGenerator
a-Hydroxy-b-methylvalerateGenerator
a-Hydroxy-b-methylvaleric acidGenerator
alpha-Hydroxy-beta-methylvalerateGenerator
Α-hydroxy-β-methylvalerateGenerator
Α-hydroxy-β-methylvaleric acidGenerator
IsoleucateGenerator
2-Hydroxy-3-methylpentanoateGenerator
2-Hydroxy-3-methylvaleric acid, monosodium salt, (S-(r*,r*))-isomerMeSH
2-Hydroxy-3-methylvaleric acid, calcium salt, (2:1), (S-(r*,r*))-isomerMeSH
alpha-Hydroxy-3-methylpentanoic acidMeSH
Chemical FormulaC6H12O3
Average Mass132.1590 Da
Monoisotopic Mass132.07864 Da
IUPAC Name2-hydroxy-3-methylpentanoic acid
Traditional Name2-hydroxy-3-methylvaleric acid
CAS Registry NumberNot Available
SMILES
CCC(C)C(O)C(O)=O
InChI Identifier
InChI=1S/C6H12O3/c1-3-4(2)5(7)6(8)9/h4-5,7H,3H2,1-2H3,(H,8,9)
InChI KeyRILPIWOPNGRASR-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
Homo sapiens (Urine)Animalia
Lagopus mutaFooDB
LeporidaeFooDB
Lepus timidusFooDB
Melanitta fuscaFooDB
Meleagris gallopavoFooDB
Nicotiana tabacumLOTUS Database
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
  • Branched fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Hydroxy fatty acid
    • 

  • Alpha-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • Secondary alcohol
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Carboxylic acid derivative
    • 

  • Alcohol
    • 

  • Hydrocarbon derivative
    • 

  • Carbonyl group
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Organooxygen compound
    • 

  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP0.74ALOGPS
logP0.86ChemAxon
logS0.05ALOGPS
pKa (Strongest Acidic)4.25ChemAxon
pKa (Strongest Basic)-3.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area57.53 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity32.44 m³·mol⁻¹ChemAxon
Polarizability13.71 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound164623  
PDB IDNot Available
ChEBI ID133083  
Good Scents IDNot Available
References
General ReferencesNot Available