Showing NP-Card for (R)-2,3-Dihydroxy-3-methylvalerate (NP0044317)

Jump To Section:
IdentificationSpectraBioTaxonomyChemoTaxonomyPhysical propertiesLinksReferencesXML
Show more...Show more...Show more...
Record Information
Version2.0
Created at2022-02-14 20:48:33 UTC
Updated at2022-03-10 22:16:34 UTC
NP-MRD IDNP0044317
Secondary Accession NumbersNone
Natural Product Identification
Common Name(R)-2,3-Dihydroxy-3-methylvalerate
Description(R)-2,3-Dihydroxy-3-methylvalerate, also known as (R)-2,3-dihydroxy-3-methylpentanoic acid or 1-keto-2-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 (R)-2,3-Dihydroxy-3-methylvalerate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. (R)-2,3-Dihydroxy-3-methylvalerate is expected to be in Cannabis as all living plants are known to produce and metabolize it.
Structure
Thumb
MOL3D MOLSDFPDBSMILESInChI

MOL for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)

  Mrv1652309042000342D          

 10  9  0  0  1  0            999 V2000
   15.4113  -13.3962    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.1244  -13.8112    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6949  -13.8112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8150  -12.6836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9967  -12.6836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8407  -13.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1206  -14.7118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9860  -13.4038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5462  -13.8112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8370  -12.5703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
Download

3D MOL for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)

     RDKit          3D

 22 21  0  0  0  0  0  0  0  0999 V2000
    2.0190   -1.1449   -0.5441 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5627   -0.1119    0.4440 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2944    0.5932    0.0070 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.0551    1.6008    1.0818 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5670    1.2090   -1.2128 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8044   -0.4316   -0.1683 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0632   -1.0366    1.0620 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0326    0.1815   -0.7088 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9896    0.7684   -1.8042 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2358    0.1156   -0.0175 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6497   -0.8244   -1.5531 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1350   -1.1786   -0.6517 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5976   -2.1425   -0.3672 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3837   -0.5341    1.4580 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3475    0.6465    0.5492 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2588    2.5674    0.5751 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7968    1.7818    1.7741 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9113    1.2141    1.6582 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3385    0.6757   -1.9916 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4402   -1.2158   -0.8548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2480   -1.9877    0.9740 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6531   -0.7459    0.2908 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  6
  3  6  1  0
  6  7  1  0
  6  8  1  0
  8 10  1  0
  8  9  2  0
  1 11  1  0
  1 12  1  0
  1 13  1  0
  2 14  1  0
  2 15  1  0
  4 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  6 20  1  6
  7 21  1  0
 10 22  1  0
M  END
Download

3D SDF for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)

  Mrv1652309042000342D          

 10  9  0  0  1  0            999 V2000
   15.4113  -13.3962    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   16.1244  -13.8112    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6949  -13.8112    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.8150  -12.6836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9967  -12.6836    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8407  -13.3962    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1206  -14.7118    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9860  -13.4038    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5462  -13.8112    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.8370  -12.5703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  1  5  1  1  0  0  0
  2  6  1  0  0  0  0
  2  7  1  6  0  0  0
  3  8  1  0  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0044317

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@@](C)(O)[C@@H](O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)/t4-,6+/m0/s1

> <INCHI_KEY>
PDGXJDXVGMHUIR-UJURSFKZSA-N

> <FORMULA>
C6H12O4

> <MOLECULAR_WEIGHT>
148.1571

> <EXACT_MASS>
148.073558872

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
14.433750785635485

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid

> <ALOGPS_LOGP>
-0.44

> <JCHEM_LOGP>
-0.2990653966666666

> <ALOGPS_LOGS>
0.52

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.109092933547867

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.930562552523404

> <JCHEM_PKA_STRONGEST_BASIC>
-3.320314291594766

> <JCHEM_POLAR_SURFACE_AREA>
77.75999999999999

> <JCHEM_REFRACTIVITY>
33.9645

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.86e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)

Download
PDB for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)
HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0      28.768 -25.006   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      30.099 -25.781   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      27.430 -25.781   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      29.521 -23.676   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      27.994 -23.676   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      31.436 -25.006   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      30.092 -27.462   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      26.107 -25.020   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      32.753 -25.781   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      31.429 -23.465   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6    7                                                  
CONECT    3    1    8                                                       
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    9   10                                                  
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END

Download
3D PDB for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)
Download
SMILES for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)
CC[C@@](C)(O)[C@@H](O)C(O)=O
Download
INCHI for NP0044317 ((R)-2,3-Dihydroxy-3-methylvalerate)
InChI=1S/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)/t4-,6+/m0/s1
Download
View in JSmol
Synonyms
Chemical FormulaC6H12O4
Average Mass148.1571 Da
Monoisotopic Mass148.07356 Da
IUPAC Name(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid
Traditional Name(2R,3R)-2,3-dihydroxy-3-methylpentanoic acid
CAS Registry Number562-43-6
SMILES
CC[C@@](C)(O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C6H12O4/c1-3-6(2,10)4(7)5(8)9/h4,7,10H,3H2,1-2H3,(H,8,9)/t4-,6+/m0/s1
InChI KeyPDGXJDXVGMHUIR-UJURSFKZSA-N
Experimental Spectra
Not Available
Predicted Spectra
Chemical Shift Submissions
Not Available
Species
Species of Origin
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
    • 

  • 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-0.44ALOGPS
logP-0.3ChemAxon
logS0.52ALOGPS
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
Polarizability14.43 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0012140  
DrugBank IDDB03675  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028798  
KNApSAcK IDNot Available
Chemspider ID395044  
KEGG Compound IDC06007  
BioCyc ID1-KETO-2-METHYLVALERATE  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound448154  
PDB IDDMV  
ChEBI ID27512  
Good Scents IDNot Available
References
General References