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Showing metabocard for D-Valine (HMDB0250806)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 07:54:54 UTC
Update Date2021-09-26 23:02:28 UTC
HMDB IDHMDB0250806
Secondary Accession NumbersNone
Metabolite Identification
Common NameD-Valine
Description(±)-Valine, also known as DL-valine or hval, 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. Thus, (±)-valine is considered to be a fatty acid (±)-Valine is an odorless tasting compound (±)-Valine is found, on average, in the highest concentration within a few different foods, such as red bell peppers (Capsicum annuum), green bell peppers (Capsicum annuum), and italian sweet red peppers (Capsicum annuum) and in a lower concentration in tofu, barleys (Hordeum vulgare), and triticales (X Triticosecale rimpaui) (±)-Valine has also been detected, but not quantified in, several different foods, such as peaches (Prunus persica), beer, peach (var.), cottonseed oil, and ucuhubas (Virola surinamensis). This could make (±)-valine a potential biomarker for the consumption of these foods (±)-Valine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on (±)-Valine. This compound has been identified in human blood as reported by (PMID: 31557052 ). D-valine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically D-Valine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0250806 (D-Valine)

  Mrv1652305221920222D          

  8  7  0  0  0  0            999 V2000
    1.2375    2.1434    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
    0.8250    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  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
    2.0625    0.7145    0.0000 N   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
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
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3D MOL for HMDB0250806 (D-Valine)

HMDB0250806
     RDKit          3D
D-Valine
 19 18  0  0  0  0  0  0  0  0999 V2000
   -1.6330    0.9577   -0.4985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442   -0.1672   -0.3870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2833   -1.2524    0.4385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6437    0.2335    0.2780 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3381    1.2773   -0.4066 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5070   -0.9673    0.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1805   -2.0477    0.8859 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7664   -0.9187   -0.2327 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5345    0.5515   -1.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9661    1.3574    0.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2821    1.8005   -1.1081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4007   -0.4946   -1.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9791   -2.2379    0.0226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9119   -1.1828    1.4581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3949   -1.1566    0.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4681    0.5890    1.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1125    1.6069    0.2266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7610    2.0852   -0.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2524   -0.0337   -0.2177 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
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  8 19  1  0
M  END
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3D SDF for HMDB0250806 (D-Valine)

  Mrv1652305221920222D          

  8  7  0  0  0  0            999 V2000
    1.2375    2.1434    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
    0.8250    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  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
    2.0625    0.7145    0.0000 N   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
  3  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  2  0  0  0  0
  8  5  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0250806

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)C(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)

> <INCHI_KEY>
KZSNJWFQEVHDMF-UHFFFAOYSA-N

> <FORMULA>
C5H11NO2

> <MOLECULAR_WEIGHT>
117.1463

> <EXACT_MASS>
117.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.279047093086072

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
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>
2.717273381855777

> <JCHEM_PKA_STRONGEST_BASIC>
9.599176382928613

> <JCHEM_POLAR_SURFACE_AREA>
63.32000000000001

> <JCHEM_REFRACTIVITY>
29.492900000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.14e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
valin

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0250806 (D-Valine)

HMDB0250806
     RDKit          3D
D-Valine
 19 18  0  0  0  0  0  0  0  0999 V2000
   -1.6330    0.9577   -0.4985 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442   -0.1672   -0.3870 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2833   -1.2524    0.4385 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6437    0.2335    0.2780 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3381    1.2773   -0.4066 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.5070   -0.9673    0.3415 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1805   -2.0477    0.8859 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7664   -0.9187   -0.2327 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5345    0.5515   -1.0020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9661    1.3574    0.4764 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2821    1.8005   -1.1081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4007   -0.4946   -1.4110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9791   -2.2379    0.0226 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9119   -1.1828    1.4581 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3949   -1.1566    0.4711 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4681    0.5890    1.3328 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1125    1.6069    0.2266 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7610    2.0852   -0.6681 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2524   -0.0337   -0.2177 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
  4  5  1  0
  4  6  1  0
  6  7  2  0
  6  8  1  0
  1  9  1  0
  1 10  1  0
  1 11  1  0
  2 12  1  0
  3 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  0
  5 17  1  0
  5 18  1  0
  8 19  1  0
M  END
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PDB for HMDB0250806 (D-Valine)

HEADER    PROTEIN                                 22-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-MAY-19         0                                  
HETATM    1  C   UNK     0       2.310   4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.000   2.667   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       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0       3.850   1.334   0.000  0.00  0.00           N+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    3                                                            
CONECT    2    3                                                            
CONECT    3    1    2    4                                                  
CONECT    4    3    5    6                                                  
CONECT    5    4    7    8                                                  
CONECT    6    4                                                            
CONECT    7    5                                                            
CONECT    8    5                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0250806 (D-Valine)

COMPND    HMDB0250806
HETATM    1  C1  UNL     1      -1.633   0.958  -0.498  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.644  -0.167  -0.387  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.283  -1.252   0.439  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.644   0.234   0.278  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.338   1.277  -0.407  1.00  0.00           N  
HETATM    6  C5  UNL     1       1.507  -0.967   0.342  1.00  0.00           C  
HETATM    7  O1  UNL     1       1.180  -2.048   0.886  1.00  0.00           O  
HETATM    8  O2  UNL     1       2.766  -0.919  -0.233  1.00  0.00           O  
HETATM    9  H1  UNL     1      -2.534   0.551  -1.002  1.00  0.00           H  
HETATM   10  H2  UNL     1      -1.966   1.357   0.476  1.00  0.00           H  
HETATM   11  H3  UNL     1      -1.282   1.801  -1.108  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.401  -0.495  -1.411  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.979  -2.238   0.023  1.00  0.00           H  
HETATM   14  H6  UNL     1      -0.912  -1.183   1.458  1.00  0.00           H  
HETATM   15  H7  UNL     1      -2.395  -1.157   0.471  1.00  0.00           H  
HETATM   16  H8  UNL     1       0.468   0.589   1.333  1.00  0.00           H  
HETATM   17  H9  UNL     1       2.112   1.607   0.227  1.00  0.00           H  
HETATM   18  H10 UNL     1       0.761   2.085  -0.668  1.00  0.00           H  
HETATM   19  H11 UNL     1       3.252  -0.034  -0.218  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3    4   12
CONECT    3   13   14   15
CONECT    4    5    6   16
CONECT    5   17   18
CONECT    6    7    7    8
CONECT    8   19
END
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SMILES for HMDB0250806 (D-Valine)

CC(C)C(N)C(O)=O
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INCHI for HMDB0250806 (D-Valine)

InChI=1S/C5H11NO2/c1-3(2)4(6)5(7)8/h3-4H,6H2,1-2H3,(H,7,8)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
2-Amino-3-methylbutanoic acidChEBI
DL-ValineChEBI
HvalChEBI
ValinChEBI
ValinaChEBI
2-Amino-3-methylbutanoateGenerator
Poly(L-val)MeSH
PolyvalineMeSH
Chemical FormulaC5H11NO2
Average Molecular Weight117.1463
Monoisotopic Molecular Weight117.078978601
IUPAC Name2-amino-3-methylbutanoic acid
Traditional Namevalin
CAS Registry NumberNot Available
SMILES
CC(C)C(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)
InChI KeyKZSNJWFQEVHDMF-UHFFFAOYSA-N
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
  • Branched fatty acid
  • Methyl-branched fatty acid
  • Fatty acid
  • Fatty acyl
  • Amino acid
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organopnictogen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Organic oxygen compound
  • Amine
  • Organic oxide
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB012740
KNApSAcK IDNot Available
Chemspider ID1148
KEGG Compound IDC16436
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkValine
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID27266
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1036191
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]