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Showing NP-Card for (r)-2,3-dihydroxy-isovalerate (NP0166283)

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Record Information
Version2.0
Created at2022-09-03 01:37:27 UTC
Updated at2022-09-03 01:37:27 UTC
NP-MRD IDNP0166283
Secondary Accession NumbersNone
Natural Product Identification
Common Name(r)-2,3-dihydroxy-isovalerate
Description(R)-2,3-Dihydroxy-isovalerate belongs to the class of organic compounds known as hydroxy fatty acids. (r)-2,3-dihydroxy-isovalerate is found in Trypanosoma brucei. These are fatty acids in which the chain bears a hydroxyl group (R)-2,3-Dihydroxy-isovalerate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (R)-2,3-Dihydroxy-isovalerate exists in all living species, ranging from bacteria to humans.
Structure
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MOL3D MOLSDFPDBSMILESInChI

MOL for NP0166283 ((r)-2,3-dihydroxy-isovalerate)


  Mrv1652309182022292D          

  9  8  0  0  0  0            999 V2000
10001.245110001.0646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.960110001.4763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.529910001.4763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.245110000.2400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.674110001.0646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.371310002.1915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.546810002.1915    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.816810001.0646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.529910002.3008    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  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3  9  2  0  0  0  0
M  END
Download

3D MOL for NP0166283 ((r)-2,3-dihydroxy-isovalerate)

     RDKit          3D

 19 18  0  0  0  0  0  0  0  0999 V2000
   -0.6340   -1.4987   -0.3644 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6035    0.0188   -0.3355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7409    0.4838    0.5488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8093    0.5229   -1.6028 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.6997    0.5306    0.2509 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8945    0.0231    1.5117 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8547    0.1895   -0.6024 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8813    0.5571   -1.7939 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9101   -0.5301   -0.1092 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0316   -1.9535    0.3807 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6662   -1.8645   -0.1905 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3209   -1.8459   -1.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7128   -0.1411    1.4631 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7140    0.3793    0.0327 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6280    1.5617    0.8334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0572    1.4944   -1.5107 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6117    1.6309    0.2943 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3557    0.4710    2.2123 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6473   -0.0293    0.3676 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  2  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
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  1
  6 18  1  0
  9 19  1  0
M  END
Download

3D SDF for NP0166283 ((r)-2,3-dihydroxy-isovalerate)


  Mrv1652309182022292D          

  9  8  0  0  0  0            999 V2000
10001.245110001.0646    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10001.960110001.4763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.529910001.4763    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.245110000.2400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.674110001.0646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10002.371310002.1915    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.546810002.1915    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.816810001.0646    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10000.529910002.3008    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  1  0  0  0
  2  5  1  0  0  0  0
  2  6  1  0  0  0  0
  2  7  1  0  0  0  0
  3  8  1  0  0  0  0
  3  9  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0166283

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c1-5(2,9)3(6)4(7)8/h3,6,9H,1-2H3,(H,7,8)/t3-/m0/s1

> <INCHI_KEY>
JTEYKUFKXGDTEU-VKHMYHEASA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.1305

> <EXACT_MASS>
134.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.481918919422833

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-0.83

> <JCHEM_LOGP>
-0.8215877916666663

> <ALOGPS_LOGS>
0.60

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.137895474801091

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7976532415810835

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2052703412545993

> <JCHEM_POLAR_SURFACE_AREA>
77.75999999999999

> <JCHEM_REFRACTIVITY>
29.4405

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.29e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-2,3-dihydroxy-isovalerate

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for NP0166283 ((r)-2,3-dihydroxy-isovalerate)

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PDB for NP0166283 ((r)-2,3-dihydroxy-isovalerate)
HEADER    PROTEIN                                 18-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-SEP-20         0                                  
HETATM    1  C   UNK     0    8668.9918668.654   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8670.3258669.422   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8667.6568669.422   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0    8668.9918667.115   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8671.6588668.654   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8671.0938670.757   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0    8669.5548670.757   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0    8666.3258668.654   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8667.6568670.962   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5    6    7                                             
CONECT    3    1    8    9                                                  
CONECT    4    1                                                            
CONECT    5    2                                                            
CONECT    6    2                                                            
CONECT    7    2                                                            
CONECT    8    3                                                            
CONECT    9    3                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END

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3D PDB for NP0166283 ((r)-2,3-dihydroxy-isovalerate)
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SMILES for NP0166283 ((r)-2,3-dihydroxy-isovalerate)
CC(C)(O)[C@@H](O)C(O)=O
Download
INCHI for NP0166283 ((r)-2,3-dihydroxy-isovalerate)
InChI=1S/C5H10O4/c1-5(2,9)3(6)4(7)8/h3,6,9H,1-2H3,(H,7,8)/t3-/m0/s1
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View in JSmol
Synonyms
ValueSource
(R)-2,3-Dihydroxy-isovaleric acidChEBI
(2R)-2,3-Dihydroxy-3-methylbutanoateKegg
(2R)-2,3-Dihydroxy-3-methylbutanoic acidGenerator
(R)-2,3-Dihydroxy-3-methylbutanoateHMDB
(R)-2,3-Dihydroxy-3-methylbutanoic acidHMDB
(R)-(-)-alpha,beta-Dihydroxyisovaleric acidHMDB
(R)-(-)-α,β-Dihydroxyisovaleric acidHMDB
(R)-2,3-Dihydroxy-isovalerateHMDB
Chemical FormulaC5H10O4
Average Mass134.1305 Da
Monoisotopic Mass134.05791 Da
IUPAC Name(2R)-2,3-dihydroxy-3-methylbutanoic acid
Traditional Name(R)-2,3-dihydroxy-isovalerate
CAS Registry NumberNot Available
SMILES
CC(C)(O)[C@@H](O)C(O)=O
InChI Identifier
InChI=1S/C5H10O4/c1-5(2,9)3(6)4(7)8/h3,6,9H,1-2H3,(H,7,8)/t3-/m0/s1
InChI KeyJTEYKUFKXGDTEU-VKHMYHEASA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Trypanosoma bruceiLOTUS Database
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-0.83ALOGPS
logP-0.82ChemAxon
logS0.6ALOGPS
pKa (Strongest Acidic)3.8ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity29.44 m³·mol⁻¹ChemAxon
Polarizability12.48 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0012141  
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028799  
KNApSAcK IDNot Available
Chemspider ID389255  
KEGG Compound IDC04272  
BioCyc IDCPD-13357  
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound440279  
PDB IDNot Available
ChEBI ID15684  
Good Scents IDNot Available
References
General References
  1. LOTUS database [Link]