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Showing NP-Card for (s)-omv (NP0226035)

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Record Information
Version2.0
Created at2022-09-06 04:57:13 UTC
Updated at2022-09-06 04:57:13 UTC
NP-MRD IDNP0226035
Secondary Accession NumbersNone
Natural Product Identification
Common Name(s)-omv
Description(S)-3-methyl-2-oxopentanoate, also known as (S)-2-oxo-3-methylpentanoic acid or (S)-OMV, belongs to the class of organic compounds known as short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms (S)-3-methyl-2-oxopentanoate is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral (S)-3-methyl-2-oxopentanoate exists in both E. (s)-omv is found in Trypanosoma brucei. (s)-omv was first documented in 1992 (PMID: 1638756). Coli (prokaryote) and yeast (eukaryote).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0226035 ((s)-omv)


  Mrv1652309092000032D          

  9  8  0  0  0  0            999 V2000
   -2.2654    0.5129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9799    0.1004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2654    1.3379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5509    0.1004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5509   -0.7245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8364    0.5129    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8364    1.3379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1220    0.1004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5924    0.5129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  3  2  0  0  0  0
  4  5  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
Download

3D MOL for NP0226035 ((s)-omv)

HMDB0000491
     RDKit          3D
3-Methyl-2-oxovaleric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.2923   -1.0065    0.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788   -1.0133   -0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0045   -0.0614    0.3639 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6130    1.3233    0.3467 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2936   -0.1281   -0.2969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4530   -0.9083   -1.2680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4178    0.6802    0.1292 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2796    1.4683    1.0999 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6544    0.6336   -0.4807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3583   -0.0201    0.9928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2283   -1.7734    1.2601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1013   -1.1540   -0.2451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5942   -2.0592   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1722   -0.7278   -1.3313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1400   -0.3230    1.4358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1194    1.5713    1.2990 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1767    2.0561    0.0841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3667    1.3692   -0.4548 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4140    0.0732   -0.0736 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  2  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  4 17  1  0
  4 18  1  0
  9 19  1  0
M  END
Download

3D SDF for NP0226035 ((s)-omv)


  Mrv1652309092000032D          

  9  8  0  0  0  0            999 V2000
   -2.2654    0.5129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9799    0.1004    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2654    1.3379    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5509    0.1004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5509   -0.7245    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8364    0.5129    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8364    1.3379    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1220    0.1004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5924    0.5129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  0  0  0  0
  8  9  1  0  0  0  0
  1  3  2  0  0  0  0
  4  5  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0226035

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H10O3/c1-3-4(2)5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9)/t4-/m0/s1

> <INCHI_KEY>
JVQYSWDUAOAHFM-BYPYZUCNSA-N

> <FORMULA>
C6H10O3

> <MOLECULAR_WEIGHT>
130.1418

> <EXACT_MASS>
130.062994186

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.983275815415249

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-3-methyl-2-oxopentanoic acid

> <ALOGPS_LOGP>
1.00

> <JCHEM_LOGP>
1.7539647436666668

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5188639238905273

> <JCHEM_PKA_STRONGEST_BASIC>
-9.724255725220358

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
31.792100000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.86e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(S)-omv

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0226035 ((s)-omv)

HMDB0000491
     RDKit          3D
3-Methyl-2-oxovaleric acid
 19 18  0  0  0  0  0  0  0  0999 V2000
   -2.2923   -1.0065    0.4778 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9788   -1.0133   -0.2953 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0045   -0.0614    0.3639 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6130    1.3233    0.3467 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2936   -0.1281   -0.2969 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4530   -0.9083   -1.2680 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4178    0.6802    0.1292 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2796    1.4683    1.0999 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6544    0.6336   -0.4807 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3583   -0.0201    0.9928 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2283   -1.7734    1.2601 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1013   -1.1540   -0.2451 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5942   -2.0592   -0.2692 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1722   -0.7278   -1.3313 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1400   -0.3230    1.4358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1194    1.5713    1.2990 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1767    2.0561    0.0841 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3667    1.3692   -0.4548 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4140    0.0732   -0.0736 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  2  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  1 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  1
  4 16  1  0
  4 17  1  0
  4 18  1  0
  9 19  1  0
M  END
Download

PDB for NP0226035 ((s)-omv)

HEADER    PROTEIN                                 09-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-20         0                                  
HETATM    1  C   UNK     0      -4.229   0.957   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -5.562   0.187   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -4.229   2.497   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -2.895   0.187   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -2.895  -1.352   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -1.561   0.957   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.561   2.497   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.228   0.187   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.106   0.957   0.000  0.00  0.00           C+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    6    5                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   16    0
END
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3D PDB for NP0226035 ((s)-omv)

COMPND    HMDB0000491
HETATM    1  C1  UNL     1      -2.292  -1.006   0.478  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.979  -1.013  -0.295  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.004  -0.061   0.364  1.00  0.00           C  
HETATM    4  C4  UNL     1      -0.613   1.323   0.347  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.294  -0.128  -0.297  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.453  -0.908  -1.268  1.00  0.00           O  
HETATM    7  C6  UNL     1       2.418   0.680   0.129  1.00  0.00           C  
HETATM    8  O2  UNL     1       2.280   1.468   1.100  1.00  0.00           O  
HETATM    9  O3  UNL     1       3.654   0.634  -0.481  1.00  0.00           O  
HETATM   10  H1  UNL     1      -2.358  -0.020   0.993  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.228  -1.773   1.260  1.00  0.00           H  
HETATM   12  H3  UNL     1      -3.101  -1.154  -0.245  1.00  0.00           H  
HETATM   13  H4  UNL     1      -0.594  -2.059  -0.269  1.00  0.00           H  
HETATM   14  H5  UNL     1      -1.172  -0.728  -1.331  1.00  0.00           H  
HETATM   15  H6  UNL     1       0.140  -0.323   1.436  1.00  0.00           H  
HETATM   16  H7  UNL     1      -1.119   1.571   1.299  1.00  0.00           H  
HETATM   17  H8  UNL     1       0.177   2.056   0.084  1.00  0.00           H  
HETATM   18  H9  UNL     1      -1.367   1.369  -0.455  1.00  0.00           H  
HETATM   19  H10 UNL     1       4.414   0.073  -0.074  1.00  0.00           H  
CONECT    1    2   10   11   12
CONECT    2    3   13   14
CONECT    3    4    5   15
CONECT    4   16   17   18
CONECT    5    6    6    7
CONECT    7    8    8    9
CONECT    9   19
END
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SMILES for NP0226035 ((s)-omv)

CC[C@H](C)C(=O)C(O)=O
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INCHI for NP0226035 ((s)-omv)

InChI=1S/C6H10O3/c1-3-4(2)5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9)/t4-/m0/s1
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View in JSmol
Synonyms
ValueSource
(3S)-2-oxo-3-Methyl-N-valeric acidChEBI
(3S)-3-Methyl-2-oxopentanoic acidChEBI
(S)-2-oxo-3-Methylpentanoic acidChEBI
(S)-3-Methyl-2-oxopentanoic acidChEBI
(S)-OMVChEBI
(3S)-3-Methyl-2-oxopentanoateKegg
(3S)-2-oxo-3-Methyl-N-valerateGenerator
(S)-2-oxo-3-MethylpentanoateGenerator
(S)-3-Methyl-2-oxopentanoateChEBI
3S-Methyl-2-oxo-pentanoateGenerator
2-Oxo-3-methyl-n-valeric acidHMDB
2-Oxo-3-methylpentanoic acidHMDB
2-Oxo-3-methylvaleric acidHMDB
2-OxoisoleucineHMDB
3-Methyl-2-ketovaleric acidHMDB
3-Methyl-2-oxopentanoic acidHMDB
3-Methyl-2-oxovaleric acidHMDB
L-2-Keto-3-MethylvalerateHMDB
L-2-keto-3-Methylvaleric acidHMDB
L-alpha-keto-beta-Methylvaleric acidHMDB
L-α-keto-β-Methylvaleric acidHMDB
alpha-keto-beta-Methylvaleric acidHMDB
alpha-Oxo-beta-methyl-n-valeric acidHMDB
alpha-Oxo-beta-methylvaleric acidHMDB
alpha-keto-beta-Methyl-n-valeric acidHMDB
α-keto-β-Methylvaleric acidHMDB
α-Oxo-β-methyl-n-valeric acidHMDB
α-Oxo-β-methylvaleric acidHMDB
α-keto-β-Methyl-n-valeric acidHMDB
Chemical FormulaC6H10O3
Average Mass130.1418 Da
Monoisotopic Mass130.06299 Da
IUPAC Name(3S)-3-methyl-2-oxopentanoic acid
Traditional Name(S)-omv
CAS Registry NumberNot Available
SMILES
CC[C@H](C)C(=O)C(O)=O
InChI Identifier
InChI=1S/C6H10O3/c1-3-4(2)5(7)6(8)9/h4H,3H2,1-2H3,(H,8,9)/t4-/m0/s1
InChI KeyJVQYSWDUAOAHFM-BYPYZUCNSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
2D NMR[1H, 13C]-HSQC NMR Spectrum (2D, 600 MHz, H2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
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 short-chain keto acids and derivatives. These are keto acids with an alkyl chain the contains less than 6 carbon atoms.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassKeto acids and derivatives
Sub ClassShort-chain keto acids and derivatives
Direct ParentShort-chain keto acids and derivatives
Alternative Parents
Substituents
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Short-chain keto acid
  • Alpha-keto acid
  • Fatty acyl
  • Alpha-hydroxy ketone
  • Ketone
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Carbonyl group
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Organooxygen compound
  • Organic oxide
  • 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
logP1ALOGPS
logP1.75ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)3.52ChemAxon
pKa (Strongest Basic)-9.7ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area54.37 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity31.79 m³·mol⁻¹ChemAxon
Polarizability12.98 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0000491
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB030164
KNApSAcK IDNot Available
Chemspider ID388419
KEGG Compound IDC00671
BioCyc ID2-KETO-3-METHYL-VALERATE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID5478
PubChem Compound439286
PDB IDNot Available
ChEBI ID15614
Good Scents IDNot Available
References
General References
  1. Wendel U, Even G, Langenbeck U, Schadewaldt P, Hummel W: Determination of (S)- and (R)-2-oxo-3-methylvaleric acid in plasma of patients with maple syrup urine disease. Clin Chim Acta. 1992 Jun 15;208(1-2):85-91. [PubMed:1638756 ]
  2. LOTUS database [Link]