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Showing NP-Card for 2,3-dihydroxy-3-methylvalerate (NP0339652)

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Record Information
Version2.0
Created at2024-09-11 22:53:48 UTC
Updated at2024-09-11 22:53:48 UTC
NP-MRD IDNP0339652
Secondary Accession NumbersNone
Natural Product Identification
Common Name2,3-dihydroxy-3-methylvalerate
Description2,3-Dihydroxy-3-methylvalerate belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. 2,3-dihydroxy-3-methylvalerate was first documented in 2009 (PMID: 19362563). Based on a literature review very few articles have been published on 2,3-dihydroxy-3-methylvalerate (PMID: 31298526).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0339652 (2,3-dihydroxy-3-methylvalerate)


  Mrv2104 05272301262D          

 10  9  0  0  0  0            999 V2000
    0.8250    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    1.8414    0.0000 O   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
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
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3D MOL for NP0339652 (2,3-dihydroxy-3-methylvalerate)

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3D SDF for NP0339652 (2,3-dihydroxy-3-methylvalerate)

  Mrv2104 05272301262D          

 10  9  0  0  0  0            999 V2000
    0.8250    2.8579    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    1.0164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    1.8414    0.0000 O   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
    2.0625    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0339652

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)

> <INCHI_KEY>
PDGXJDXVGMHUIR-UHFFFAOYNA-N

> <FORMULA>
C6H12O4

> <MOLECULAR_WEIGHT>
148.158

> <EXACT_MASS>
148.073558866

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.410782667569743

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,3-dihydroxy-3-methylpentanoic acid

> <JCHEM_LOGP>
-0.2990653966666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.109092933547869

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.930562552523404

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3203142915947663

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
33.9645

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
2,3-dihydroxy-3-methylvalerate

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0339652 (2,3-dihydroxy-3-methylvalerate)
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PDB for NP0339652 (2,3-dihydroxy-3-methylvalerate)
HEADER    PROTEIN                                 27-MAY-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-23         0                                  
HETATM    1  C   UNK     0       1.540   5.335   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.770   4.001   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.206   1.897   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       2.874   3.437   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       3.850   1.334   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5    6                                             
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6    3    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

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3D PDB for NP0339652 (2,3-dihydroxy-3-methylvalerate)
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SMILES for NP0339652 (2,3-dihydroxy-3-methylvalerate)
CCC(C)(O)C(O)C(O)=O
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INCHI for NP0339652 (2,3-dihydroxy-3-methylvalerate)
InChI=1/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)
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Synonyms
ValueSource
2,3-Dihydroxy-3-methylvaleric acidGenerator
Chemical FormulaC6H12O4
Average Mass148.1580 Da
Monoisotopic Mass148.07356 Da
IUPAC Name2,3-dihydroxy-3-methylpentanoic acid
Traditional Name2,3-dihydroxy-3-methylvalerate
CAS Registry NumberNot Available
SMILES
CCC(C)(O)C(O)C(O)=O
InChI Identifier
InChI=1/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)
InChI KeyPDGXJDXVGMHUIR-UHFFFAOYNA-N
Experimental Spectra
Not Available
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
Chemical Taxonomy
DescriptionThis compound 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
    • 

  • Short-chain hydroxy acid
    • 

  • Hydroxy fatty acid
    • 

  • Alpha-hydroxy acid
    • 

  • Hydroxy acid
    • 

  • Monosaccharide
    • 

  • Tertiary alcohol
    • 

  • 1,2-diol
    • 

  • Secondary alcohol
    • 

  • Carboxylic acid derivative
    • 

  • Carboxylic acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organic oxygen compound
    • 

  • Carbonyl group
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Alcohol
    • 

  • Organooxygen 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
logP-0.3ChemAxon
pKa (Strongest Acidic)3.93ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity33.96 m³·mol⁻¹ChemAxon
Polarizability14.41 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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Lee D, Hong J, Kim KJ: Crystal Structure and Biochemical Characterization of Ketol-Acid Reductoisomerase from Corynebacterium glutamicum. J Agric Food Chem. 2019 Aug 7;67(31):8527-8535. doi: 10.1021/acs.jafc.9b03262.  Epub 2019 Jul 25. [PubMed:31298526  ] 
  2. Leung EW, Guddat LW: Conformational changes in a plant ketol-acid reductoisomerase upon Mg(2+) and NADPH binding as revealed by two crystal structures. J Mol Biol. 2009 May 29;389(1):167-82. doi: 10.1016/j.jmb.2009.04.012. Epub 2009  Apr 9. [PubMed:19362563  ]