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Showing metabocard for Norvaline (HMDB0013716)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2012-05-18 14:04:04 UTC
Update Date2023-02-21 17:18:01 UTC
HMDB IDHMDB0013716
Secondary Accession Numbers
  • HMDB13716
Metabolite Identification
Common NameNorvaline
DescriptionNorvaline is a non-proteinogenic branched-chain amino acid with the chemical formula C5H11NO2, isomeric with valine. It has previously been reported to be a natural component of an antifungal peptide of Bacillus subtilis. Norvaline and other modified branched chain amino acids have received attention in recent studies, as they appear to be incorporated in some recombinant proteins found in E. coli. This amino acid is often made synthetically.
Structure
Data?1676999881
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013716 (Norvaline)

ChEBI
  Mrv1652302102020392D          

  8  7  0  0  1  0            999 V2000
    6.4363   -3.2155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7187   -3.6222    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0009   -3.2155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2833   -3.6222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5536   -3.2155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4363   -2.3782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1421   -3.6222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7187   -4.4595    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  7  1  1  0  0  0  0
  6  1  2  0  0  0  0
  3  2  1  0  0  0  0
  2  8  1  6  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
M  END
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3D MOL for HMDB0013716 (Norvaline)

HMDB0013716
     RDKit          3D
Norvaline
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.6982    0.0086   -0.4230 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4230   -0.2447    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3281    0.4988   -0.2794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0166    0.3639    0.3936 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9539    1.1460   -0.3900 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4980   -1.0177    0.4773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8936   -1.9353    1.0998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6777   -1.3751   -0.1483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309   -0.5744   -1.3701 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5971   -0.2204    0.1499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6953    1.0803   -0.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6268    0.2417    1.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2782   -1.3177    0.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2229    0.2179   -1.3454 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5840    1.5786   -0.2685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9474    0.7538    1.4334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6175    1.2721   -1.3769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8881    0.6586   -0.4845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5918   -1.1349    0.1974 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
  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
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  5 18  1  0
  8 19  1  0
M  END
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3D SDF for HMDB0013716 (Norvaline)

ChEBI
  Mrv1652302102020392D          

  8  7  0  0  1  0            999 V2000
    6.4363   -3.2155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7187   -3.6222    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.0009   -3.2155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2833   -3.6222    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5536   -3.2155    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4363   -2.3782    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1421   -3.6222    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7187   -4.4595    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  7  1  1  0  0  0  0
  6  1  2  0  0  0  0
  3  2  1  0  0  0  0
  2  8  1  6  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013716

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1

> <INCHI_KEY>
SNDPXSYFESPGGJ-SCSAIBSYSA-N

> <FORMULA>
C5H11NO2

> <MOLECULAR_WEIGHT>
117.1463

> <EXACT_MASS>
117.078978601

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
12.50887298672354

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-aminopentanoic acid

> <ALOGPS_LOGP>
-2.04

> <JCHEM_LOGP>
-1.8733752172778175

> <ALOGPS_LOGS>
0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7136746618065293

> <JCHEM_PKA_STRONGEST_BASIC>
9.526860379684688

> <JCHEM_POLAR_SURFACE_AREA>
63.31999999999999

> <JCHEM_REFRACTIVITY>
29.6223

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.12e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-(-)-norvaline

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0013716 (Norvaline)

HMDB0013716
     RDKit          3D
Norvaline
 19 18  0  0  0  0  0  0  0  0999 V2000
    2.6982    0.0086   -0.4230 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4230   -0.2447    0.3935 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3281    0.4988   -0.2794 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0166    0.3639    0.3936 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9539    1.1460   -0.3900 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4980   -1.0177    0.4773 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8936   -1.9353    1.0998 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6777   -1.3751   -0.1483 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6309   -0.5744   -1.3701 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5971   -0.2204    0.1499 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6953    1.0803   -0.7370 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6268    0.2417    1.3856 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2782   -1.3177    0.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2229    0.2179   -1.3454 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5840    1.5786   -0.2685 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9474    0.7538    1.4334 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6175    1.2721   -1.3769 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8881    0.6586   -0.4845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5918   -1.1349    0.1974 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
  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
  2 13  1  0
  3 14  1  0
  3 15  1  0
  4 16  1  1
  5 17  1  0
  5 18  1  0
  8 19  1  0
M  END
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PDB for HMDB0013716 (Norvaline)

HEADER    PROTEIN                                 10-FEB-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: ChEBI                                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-FEB-20         0                                  
HETATM    1  C   UNK     0      12.014  -6.002   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.675  -6.761   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       9.335  -6.002   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.995  -6.761   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       6.633  -6.002   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      12.014  -4.439   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      13.332  -6.761   0.000  0.00  0.00           O+0
HETATM    8  N   UNK     0      10.675  -8.324   0.000  0.00  0.00           N+0
CONECT    1    2    7    6                                                  
CONECT    2    1    3    8                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    1                                                            
CONECT    7    1                                                            
CONECT    8    2                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for HMDB0013716 (Norvaline)

COMPND    HMDB0013716
HETATM    1  C1  UNL     1       2.698   0.009  -0.423  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.423  -0.245   0.393  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.328   0.499  -0.279  1.00  0.00           C  
HETATM    4  C4  UNL     1      -1.017   0.364   0.394  1.00  0.00           C  
HETATM    5  N1  UNL     1      -1.954   1.146  -0.390  1.00  0.00           N  
HETATM    6  C5  UNL     1      -1.498  -1.018   0.477  1.00  0.00           C  
HETATM    7  O1  UNL     1      -0.894  -1.935   1.100  1.00  0.00           O  
HETATM    8  O2  UNL     1      -2.678  -1.375  -0.148  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.631  -0.574  -1.370  1.00  0.00           H  
HETATM   10  H2  UNL     1       3.597  -0.220   0.150  1.00  0.00           H  
HETATM   11  H3  UNL     1       2.695   1.080  -0.737  1.00  0.00           H  
HETATM   12  H4  UNL     1       1.627   0.242   1.386  1.00  0.00           H  
HETATM   13  H5  UNL     1       1.278  -1.318   0.506  1.00  0.00           H  
HETATM   14  H6  UNL     1       0.223   0.218  -1.345  1.00  0.00           H  
HETATM   15  H7  UNL     1       0.584   1.579  -0.269  1.00  0.00           H  
HETATM   16  H8  UNL     1      -0.947   0.754   1.433  1.00  0.00           H  
HETATM   17  H9  UNL     1      -1.617   1.272  -1.377  1.00  0.00           H  
HETATM   18  H10 UNL     1      -2.888   0.659  -0.485  1.00  0.00           H  
HETATM   19  H11 UNL     1      -3.592  -1.135   0.197  1.00  0.00           H  
CONECT    1    2    9   10   11
CONECT    2    3   12   13
CONECT    3    4   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 HMDB0013716 (Norvaline)

CCC[C@@H](N)C(O)=O
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INCHI for HMDB0013716 (Norvaline)

InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H11NO2
Average Molecular Weight117.1463
Monoisotopic Molecular Weight117.078978601
IUPAC Name(2R)-2-aminopentanoic acid
Traditional NameD-(-)-norvaline
CAS Registry Number760-78-1
SMILES
CCC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C5H11NO2/c1-2-3-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1
InChI KeySNDPXSYFESPGGJ-SCSAIBSYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentD-alpha-amino acids
Alternative Parents
Substituents
  • 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
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Primary aliphatic amine
  • Carbonyl group
  • Organic nitrogen compound
  • Amine
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point303 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility83.9 mg/mL at 25 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M+H]+Not Available120.8http://allccs.zhulab.cn/database/detail?ID=AllCCS00002163
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot Available
Normal
      Not Available
 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineDetected and Quantified0.02 umol/mmol creatinineAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDC00018307
Chemspider ID388660
KEGG Compound IDC01799
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNorvaline
METLIN IDNot Available
PubChem Compound439575
PDB IDNot Available
ChEBI ID28804
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available