Showing metabocard for D-Lysine (MMDBc0000240)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:59 UTC
Update Date2022-08-31 00:15:58 UTC
Metabolite IDMMDBc0000240
Metabolite Identification
Common NameD-Lysine
DescriptionD-Lysine is an essential amino acid. It is often added to animal feed.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x000055c798b8dac0>


  Mrv1652303202019002D          

 10  9  0  0  0  0            999 V2000
 9996.8368 9997.7078    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9997.5515 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2654 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9809 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6963 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.4097 9998.1199    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.1221 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.4074 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.1221 9998.9445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8368 9996.8826    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x000055c798b8dac0>

HMDB0003405
     RDKit          3D
D-Lysine
 24 23  0  0  0  0  0  0  0  0999 V2000
    3.1722   -0.2145   -0.1566 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1585   -0.7184    0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3106    0.4891    1.1661 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6744    1.1229   -0.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2174    0.1736   -0.7876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3541   -0.3378    0.0639 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1553    0.8087    0.4976 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2169   -1.1877   -0.8056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7335   -2.2440   -1.3013 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -0.8811   -1.1015 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3379    0.7937   -0.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0456   -0.5547   -1.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5844   -1.2203    1.6260 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5153   -1.4161    0.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0233    1.1996    1.6328 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5336    0.2013    1.8916 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5026    1.3975   -0.7647 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1807    2.0665    0.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7024    0.7576   -1.6211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3386   -0.6315   -1.2662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0192   -0.8803    0.9575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0695    1.5856   -0.1756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1556    0.5510    0.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2268   -0.8607   -0.3823 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
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  1
  7 22  1  0
  7 23  1  0
 10 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x000055c798b8dac0>


  Mrv1652303202019002D          

 10  9  0  0  0  0            999 V2000
 9996.8368 9997.7078    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
 9997.5515 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2654 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9809 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.6963 9997.7078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.4097 9998.1199    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.1221 9998.1199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.4074 9997.7078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.1221 9998.9445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9996.8368 9996.8826    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  7  1  0  0  0  0
  1 10  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  1  0  0  0  0
  7  9  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000240

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1

> <INCHI_KEY>
KDXKERNSBIXSRK-RXMQYKEDSA-N

> <FORMULA>
C6H14N2O2

> <MOLECULAR_WEIGHT>
146.19

> <EXACT_MASS>
146.105527699

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
15.90981981318644

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2,6-diaminohexanoic acid

> <ALOGPS_LOGP>
-3.76

> <JCHEM_LOGP>
-3.2145347205442243

> <ALOGPS_LOGS>
-0.14

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7382862451336982

> <JCHEM_PKA_STRONGEST_BASIC>
10.28806162304154

> <JCHEM_POLAR_SURFACE_AREA>
89.34

> <JCHEM_REFRACTIVITY>
37.8095

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.05e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
D-lysine

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x000055c798b8dac0>

HMDB0003405
     RDKit          3D
D-Lysine
 24 23  0  0  0  0  0  0  0  0999 V2000
    3.1722   -0.2145   -0.1566 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1585   -0.7184    0.7473 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3106    0.4891    1.1661 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6744    1.1229   -0.0532 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2174    0.1736   -0.7876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3541   -0.3378    0.0639 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1553    0.8087    0.4976 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2169   -1.1877   -0.8056 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7335   -2.2440   -1.3013 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5269   -0.8811   -1.1015 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3379    0.7937   -0.0789 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0456   -0.5547   -1.1329 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5844   -1.2203    1.6260 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5153   -1.4161    0.2011 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0233    1.1996    1.6328 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5336    0.2013    1.8916 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5026    1.3975   -0.7647 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1807    2.0665    0.2061 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7024    0.7576   -1.6211 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3386   -0.6315   -1.2662 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0192   -0.8803    0.9575 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0695    1.5856   -0.1756 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1556    0.5510    0.6375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2268   -0.8607   -0.3823 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
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  8 10  1  0
  1 11  1  0
  1 12  1  0
  2 13  1  0
  2 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  0
  5 20  1  0
  6 21  1  1
  7 22  1  0
  7 23  1  0
 10 24  1  0
M  END
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PDB for #<Metabolite:0x000055c798b8dac0>

HEADER    PROTEIN                                 20-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAR-20         0                                  
HETATM    1  C   UNK     0    8660.7628662.388   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8662.0968663.157   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8663.4298662.388   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0    8664.7648663.157   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0    8666.1008662.388   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8667.4318663.157   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8659.4288663.157   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8658.0948662.388   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0    8659.4288664.696   0.000  0.00  0.00           O+0
HETATM   10  N   UNK     0    8660.7628660.848   0.000  0.00  0.00           N+0
CONECT    1    2    7   10                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
CONECT    7    1    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    1                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x000055c798b8dac0>

COMPND    HMDB0003405
HETATM    1  N1  UNL     1       3.172  -0.215  -0.157  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.158  -0.718   0.747  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.311   0.489   1.166  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.674   1.123  -0.053  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.217   0.174  -0.788  1.00  0.00           C  
HETATM    6  C5  UNL     1      -1.354  -0.338   0.064  1.00  0.00           C  
HETATM    7  N2  UNL     1      -2.155   0.809   0.498  1.00  0.00           N  
HETATM    8  C6  UNL     1      -2.217  -1.188  -0.806  1.00  0.00           C  
HETATM    9  O1  UNL     1      -1.734  -2.244  -1.301  1.00  0.00           O  
HETATM   10  O2  UNL     1      -3.527  -0.881  -1.102  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.338   0.794  -0.079  1.00  0.00           H  
HETATM   12  H2  UNL     1       3.046  -0.555  -1.133  1.00  0.00           H  
HETATM   13  H3  UNL     1       2.584  -1.220   1.626  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.515  -1.416   0.201  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.023   1.200   1.633  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.534   0.201   1.892  1.00  0.00           H  
HETATM   17  H7  UNL     1       1.503   1.397  -0.765  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.181   2.067   0.206  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.702   0.758  -1.621  1.00  0.00           H  
HETATM   20  H10 UNL     1       0.339  -0.632  -1.266  1.00  0.00           H  
HETATM   21  H11 UNL     1      -1.019  -0.880   0.958  1.00  0.00           H  
HETATM   22  H12 UNL     1      -2.069   1.586  -0.176  1.00  0.00           H  
HETATM   23  H13 UNL     1      -3.156   0.551   0.637  1.00  0.00           H  
HETATM   24  H14 UNL     1      -4.227  -0.861  -0.382  1.00  0.00           H  
CONECT    1    2   11   12
CONECT    2    3   13   14
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6   19   20
CONECT    6    7    8   21
CONECT    7   22   23
CONECT    8    9    9   10
CONECT   10   24
END
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SMILES for #<Metabolite:0x000055c798b8dac0>

NCCCC[C@@H](N)C(O)=O
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INCHI for #<Metabolite:0x000055c798b8dac0>

InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1
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Synonyms
ValueSource
(R)-2,6-Diaminohexanoic acidChEBI
D-2,6-Diaminohexanoic acidChEBI
D-LysinChEBI
DLYChEBI
(R)-2,6-DiaminohexanoateGenerator
D-2,6-DiaminohexanoateGenerator
Molecular FormulaC6H14N2O2
Average Mass146.19
Monoisotopic Mass146.105527699
IUPAC Name(2R)-2,6-diaminohexanoic acid
Traditional NameD-lysine
CAS Registry Number923-27-3
SMILES
NCCCC[C@@H](N)C(O)=O
InChI Identifier
InChI=1S/C6H14N2O2/c7-4-2-1-3-5(8)6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m1/s1
InChI KeyKDXKERNSBIXSRK-RXMQYKEDSA-N