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Showing NP-Card for D-Valine (NP0333300)

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Record Information
Version2.0
Created at2024-05-24 16:53:57 UTC
Updated at2024-09-03 04:21:53 UTC
NP-MRD IDNP0333300
Natural Product DOIhttps://doi.org/10.57994/2655
Secondary Accession NumbersNone
Natural Product Identification
Common NameD-Valine
DescriptionD-Valine, also known as (R)-valine or D-valin, belongs to the class of organic compounds known as valine and derivatives. Valine and derivatives are compounds containing valine or a derivative thereof resulting from reaction of valine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. D-Valine is a very strong basic compound (based on its pKa). D-Valine may be a unique S. D-Valine was first documented in 1957 (PMID: 13465080). Cerevisiae (yeast) metabolite (PMID: 23085840) (PMID: 236834) (PMID: 7118128).
Structure
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MOLSDFPDBSMILESInChI

MOL for NP0333300 (D-Valine)


  Mrv0541 02241222502D          

  8  7  0  0  1  0            999 V2000
    1.2375    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
    0.0000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   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
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
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3D MOL for NP0333300 (D-Valine)

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3D SDF for NP0333300 (D-Valine)

  Mrv0541 02241222502D          

  8  7  0  0  1  0            999 V2000
    1.2375    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
    0.0000    1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.0625    0.7145    0.0000 N   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
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  4  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0333300

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m1/s1

> <INCHI_KEY>
KZSNJWFQEVHDMF-SCSAIBSYSA-N

> <FORMULA>
C5H11NO2

> <MOLECULAR_WEIGHT>
117.1463

> <EXACT_MASS>
117.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
12.189707310409453

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-amino-3-methylbutanoic acid

> <ALOGPS_LOGP>
-2.29

> <JCHEM_LOGP>
-1.953136464200883

> <ALOGPS_LOGS>
0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7172733818557804

> <JCHEM_PKA_STRONGEST_BASIC>
9.59917638292861

> <JCHEM_POLAR_SURFACE_AREA>
63.32

> <JCHEM_REFRACTIVITY>
29.492900000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.14e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-valine

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for NP0333300 (D-Valine)
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PDB for NP0333300 (D-Valine)
HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.540   2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+0
HETATM    6  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5    6                                                  
CONECT    5    4                                                            
CONECT    6    4    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END

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3D PDB for NP0333300 (D-Valine)
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SMILES for NP0333300 (D-Valine)
CC(C)[C@@H](N)C(O)=O
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INCHI for NP0333300 (D-Valine)
InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m1/s1
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Synonyms
ValueSource
(2R)-2-Amino-3-methylbutanoic acidChEBI
(R)-2-Amino-3-methylbutyric acidChEBI
(R)-ValineChEBI
D-ValinChEBI
DVAChEBI
(2R)-2-Amino-3-methylbutanoateGenerator
(R)-2-Amino-3-methylbutyrateGenerator
Chemical FormulaC5H11NO2
Average Mass117.1463 Da
Monoisotopic Mass117.07898 Da
IUPAC Name(2R)-2-amino-3-methylbutanoic acid
Traditional NameD-valine
CAS Registry NumberNot Available
SMILES
CC(C)[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)/t4-/m1/s1
InChI KeyKZSNJWFQEVHDMF-SCSAIBSYSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-24View Spectrum
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-24View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-24View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-24View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-24View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600, D2O, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-05-24View Spectrum
Species
Species of OriginNot Available
Chemical Taxonomy
Description Belongs to the class of organic compounds known as valine and derivatives. Valine and derivatives are compounds containing valine or a derivative thereof resulting from reaction of valine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassCarboxylic acids and derivatives  
Sub ClassAmino acids, peptides, and analogues  
Direct ParentValine and derivatives  
Alternative Parents
Substituents
  • Valine or derivatives
    • 

  • Alpha-amino acid
    • 

  • D-alpha-amino acid
    • 

  • Branched fatty acid
    • 

  • Methyl-branched fatty acid
    • 

  • Fatty acid
    • 

  • Fatty acyl
    • 

  • Amino acid
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Carboxylic acid
    • 

  • Organic oxide
    • 

  • Organopnictogen compound
    • 

  • Primary amine
    • 

  • Organooxygen compound
    • 

  • Organonitrogen compound
    • 

  • Primary aliphatic amine
    • 

  • Carbonyl group
    • 

  • Organic oxygen compound
    • 

  • Amine
    • 

  • Organic nitrogen compound
    • 

  • Hydrocarbon derivative
    • 

  • 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-2.3ALOGPS
logP-2ChemAxon
logS0.26ALOGPS
pKa (Strongest Acidic)2.72ChemAxon
pKa (Strongest Basic)9.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity29.49 m³·mol⁻¹ChemAxon
Polarizability12.19 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 IDC06417  
BioCyc IDCPD-3642  
BiGG IDNot Available
Wikipedia LinkValine  
METLIN IDNot Available
PubChem Compound71563  
PDB IDNot Available
ChEBI ID27477  
Good Scents IDNot Available
References
General References
  1. Authors unspecified: UTILIZATION of D-valine. Nutr Rev. 1957 Sep;15(9):280-1. doi: 10.1111/j.1753-4887.1957.tb00599.x. [PubMed:13465080  ] 
  2. Gisby MF, Mudd EA, Day A: Growth of transplastomic cells expressing D-amino acid oxidase in chloroplasts is tolerant to D-alanine and inhibited by D-valine. Plant Physiol. 2012 Dec;160(4):2219-26. doi: 10.1104/pp.112.204107. Epub 2012 Oct  18. [PubMed:23085840  ] 
  3. Gilbert SF, Migeon BR: D-valine as a selective agent for normal human and rodent epithelial cells in culture. Cell. 1975 May;5(1):11-7. doi: 10.1016/0092-8674(75)90086-0. [PubMed:236834  ] 
  4. Ehmann UK, Misfeldt DS: Mouse mammary cells in D-valine medium. In Vitro. 1982 Apr;18(4):407-14. doi: 10.1007/BF02796342. [PubMed:7118128  ]