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

Xenobiotic
Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-07-26 19:02:47 UTC
Update Date2025-10-07 16:09:48 UTC
Metabolite IDMMDBc0057085
Metabolite Identification
Common NameD-2-aminopentanoic acid
DescriptionD-2-aminopentanoic acid is a non-proteinogenic amino acid belonging to the class of amino acids. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and potential applications.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9ac01bba40>

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:0x00007f9ac01bba40>

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:0x00007f9ac01bba40>

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:0x00007f9ac01bba40>

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:0x00007f9ac01bba40>

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:0x00007f9ac01bba40>

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:0x00007f9ac01bba40>

CCC[C@@H](N)C(O)=O
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INCHI for #<Metabolite:0x00007f9ac01bba40>

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