Showing metabocard for D-2-aminopentanoic acid (MMDBc0057085)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-07-26 19:02:47 UTC
Update Date2024-10-17 08:43:32 UTC
Metabolite IDMMDBc0057085
Metabolite Identification
Common NameD-2-aminopentanoic acid
DescriptionNorvaline, also known as (R)-norvaline or D-ape, 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. Norvaline exists in all eukaryotes, ranging from yeast to plants to humans. Based on a literature review very few articles have been published on Norvaline.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645ca2fe458>

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 #<Metabolite:0x00005645ca2fe458>

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 #<Metabolite:0x00005645ca2fe458>

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>
MMDBc0057085

> <DATABASE_NAME>
MIME

> <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

$$$$
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3D-SDF for #<Metabolite:0x00005645ca2fe458>

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 #<Metabolite:0x00005645ca2fe458>

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 #<Metabolite:0x00005645ca2fe458>

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 #<Metabolite:0x00005645ca2fe458>

CCC[C@@H](N)C(O)=O
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INCHI for #<Metabolite:0x00005645ca2fe458>

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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Synonyms
ValueSource
(R)-NorvalineChEBI
D-2-Aminovaleric acidChEBI
D-ApeChEBI
D-NorvalineChEBI
D-NvaChEBI
D-2-Aminopentanoic acidKegg
D-2-AminovalerateGenerator
D-2-AminopentanoateGenerator
(.+-.)-norvalineHMDB
(.+/-.)-norvalineHMDB
2-Amino-DL-valeric acidHMDB
2-Aminopentanoic acidsHMDB
2-Aminovaleric acidHMDB
2-Aminovaleric acidsHMDB
alpha -DL-Aminopentanoic acidHMDB
alpha-Aminopentanoic acidHMDB
alpha-Aminovaleric acidHMDB
alpha-DL-Aminopentanoic acidHMDB
DL-2-Aminopentanoic acidHMDB
DL-alpha -Aminovaleric acidHMDB
DL-alpha-Amino-N-valenic acidHMDB
DL-alpha-Aminovaleric acidHMDB
DL-NorvalineHMDB
Norvaline (acd/name 4.0)HMDB
NorvalinesHMDB
Molecular FormulaC5H11NO2
Average Mass117.1463
Monoisotopic Mass117.078978601
IUPAC Name(2R)-2-aminopentanoic acid
Traditional NameD-(-)-norvaline
CAS Registry NumberNot Available
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