Showing metabocard for (3S)-3,6-Diaminohexanoate (MMDBc0049941)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:46:43 UTC
Update Date2025-01-15 22:35:59 UTC
Metabolite IDMMDBc0049941
Metabolite Identification
Common Name(3S)-3,6-Diaminohexanoate
Description(3S)-3,6-Diaminohexanoate is found in the lysine degradation pathway. (3S)-3,6-Diaminohexanoate is created from L-lysine through the action of lysine 2,3-aminomutase [EC:5.4.3.2]. (3S)-3,6-Diaminohexanoate is then reversibly converted to (3S,5S)-3,5-Diaminohexanoate by beta-lysine 5,6-aminomutase [EC:5.4.3.3].
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f9250fc91c8>


  Mrv0541 02241203392D          

 10  9  0  0  1  0            999 V2000
   19.6549   -9.3726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.6549   -8.5476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9404   -9.7851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3694   -7.3101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3694   -8.1351    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.6549   -6.8976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9404  -10.6102    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.0838   -8.5476    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.6549   -6.0726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9404   -7.3101    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f9250fc91c8>

HMDB0012114
     RDKit          3D
(3S)-3,6-Diaminohexanoate
 24 23  0  0  0  0  0  0  0  0999 V2000
    3.4048    0.2569    1.3149 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1839   -0.1399    0.6080 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6941    0.9762   -0.2649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4776    0.7050   -1.0683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7393    0.3715   -0.2682 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5959   -0.7992    0.5305 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9448    0.1691   -1.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1384   -0.1599   -0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2458   -0.3669   -0.9494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489   -0.2608    1.0108 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3423    0.1310    2.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2292   -0.2592    0.9554 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4165   -1.0572    0.0361 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4597   -0.4227    1.4205 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5206    1.2600   -0.9674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5463    1.8790    0.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7208   -0.1116   -1.8039 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2246    1.5752   -1.7251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9630    1.2178    0.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9159   -0.7295    1.5034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8413   -1.6897    0.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7065   -0.7255   -1.7981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1029    1.0013   -1.8594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8777    0.0760    1.6184 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
  5  7  1  0
  7  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  1
  6 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
 10 24  1  0
M  END
Download

3D SDF for #<Metabolite:0x00007f9250fc91c8>


  Mrv0541 02241203392D          

 10  9  0  0  1  0            999 V2000
   19.6549   -9.3726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.6549   -8.5476    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9404   -9.7851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3694   -7.3101    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3694   -8.1351    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.6549   -6.8976    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9404  -10.6102    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.0838   -8.5476    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.6549   -6.0726    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.9404   -7.3101    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  2  1  0  0  0  0
  2  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  0  0  0  0
  6 10  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049941

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H14N2O2/c7-3-1-2-5(8)4-6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1

> <INCHI_KEY>
QKEWQOJCHPFEAF-YFKPBYRVSA-N

> <FORMULA>
C6H14N2O2

> <MOLECULAR_WEIGHT>
146.1876

> <EXACT_MASS>
146.105527702

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
15.918845444954371

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-3,6-diaminohexanoic acid

> <ALOGPS_LOGP>
-3.56

> <JCHEM_LOGP>
-3.6856497783945392

> <ALOGPS_LOGS>
-0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.249857453142085

> <JCHEM_PKA_STRONGEST_BASIC>
10.70976217116247

> <JCHEM_POLAR_SURFACE_AREA>
89.34

> <JCHEM_REFRACTIVITY>
37.8328

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.93e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-3,6-diaminohexanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f9250fc91c8>

HMDB0012114
     RDKit          3D
(3S)-3,6-Diaminohexanoate
 24 23  0  0  0  0  0  0  0  0999 V2000
    3.4048    0.2569    1.3149 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1839   -0.1399    0.6080 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6941    0.9762   -0.2649 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4776    0.7050   -1.0683 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7393    0.3715   -0.2682 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5959   -0.7992    0.5305 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9448    0.1691   -1.1710 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1384   -0.1599   -0.3512 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2458   -0.3669   -0.9494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1489   -0.2608    1.0108 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3423    0.1310    2.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2292   -0.2592    0.9554 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4165   -1.0572    0.0361 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4597   -0.4227    1.4205 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5206    1.2600   -0.9674 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5463    1.8790    0.4022 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7208   -0.1116   -1.8039 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2246    1.5752   -1.7251 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9630    1.2178    0.4293 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9159   -0.7295    1.5034 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8413   -1.6897    0.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7065   -0.7255   -1.7981 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1029    1.0013   -1.8594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8777    0.0760    1.6184 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
  5  7  1  0
  7  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  1
  6 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
 10 24  1  0
M  END
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PDB for #<Metabolite:0x00007f9250fc91c8>

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      36.689 -17.496   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      36.689 -15.956   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      35.355 -18.266   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      38.023 -13.646   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      38.023 -15.186   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      36.689 -12.876   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      35.355 -19.806   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      39.356 -15.956   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      36.689 -11.336   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      35.355 -13.646   0.000  0.00  0.00           O+0
CONECT    1    3    2                                                       
CONECT    2    1    5                                                       
CONECT    3    1    7                                                       
CONECT    4    5    6                                                       
CONECT    5    2    4    8                                                  
CONECT    6    4    9   10                                                  
CONECT    7    3                                                            
CONECT    8    5                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
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3D PDB for #<Metabolite:0x00007f9250fc91c8>

COMPND    HMDB0012114
HETATM    1  N1  UNL     1       3.405   0.257   1.315  1.00  0.00           N  
HETATM    2  C1  UNL     1       2.184  -0.140   0.608  1.00  0.00           C  
HETATM    3  C2  UNL     1       1.694   0.976  -0.265  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.478   0.705  -1.068  1.00  0.00           C  
HETATM    5  C4  UNL     1      -0.739   0.372  -0.268  1.00  0.00           C  
HETATM    6  N2  UNL     1      -0.596  -0.799   0.531  1.00  0.00           N  
HETATM    7  C5  UNL     1      -1.945   0.169  -1.171  1.00  0.00           C  
HETATM    8  C6  UNL     1      -3.138  -0.160  -0.351  1.00  0.00           C  
HETATM    9  O1  UNL     1      -4.246  -0.367  -0.949  1.00  0.00           O  
HETATM   10  O2  UNL     1      -3.149  -0.261   1.011  1.00  0.00           O  
HETATM   11  H1  UNL     1       3.342   0.131   2.338  1.00  0.00           H  
HETATM   12  H2  UNL     1       4.229  -0.259   0.955  1.00  0.00           H  
HETATM   13  H3  UNL     1       2.417  -1.057   0.036  1.00  0.00           H  
HETATM   14  H4  UNL     1       1.460  -0.423   1.420  1.00  0.00           H  
HETATM   15  H5  UNL     1       2.521   1.260  -0.967  1.00  0.00           H  
HETATM   16  H6  UNL     1       1.546   1.879   0.402  1.00  0.00           H  
HETATM   17  H7  UNL     1       0.721  -0.112  -1.804  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.225   1.575  -1.725  1.00  0.00           H  
HETATM   19  H9  UNL     1      -0.963   1.218   0.429  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.916  -0.730   1.503  1.00  0.00           H  
HETATM   21  H11 UNL     1      -0.841  -1.690   0.059  1.00  0.00           H  
HETATM   22  H12 UNL     1      -1.706  -0.725  -1.798  1.00  0.00           H  
HETATM   23  H13 UNL     1      -2.103   1.001  -1.859  1.00  0.00           H  
HETATM   24  H14 UNL     1      -3.878   0.076   1.618  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    7   19
CONECT    6   20   21
CONECT    7    8   22   23
CONECT    8    9    9   10
CONECT   10   24
END
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SMILES for #<Metabolite:0x00007f9250fc91c8>

NCCC[C@H](N)CC(O)=O
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INCHI for #<Metabolite:0x00007f9250fc91c8>

InChI=1S/C6H14N2O2/c7-3-1-2-5(8)4-6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1
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Synonyms
ValueSource
L-beta-LysineChEBI
L-b-LysineGenerator
L-Β-lysineGenerator
(3S)-3,6-Diaminohexanoic acidGenerator
3,6-diamino-HexanoateHMDB
3,6-diamino-Hexanoic acidHMDB
3,6-DiaminohexanoateHMDB
3,6-Diaminohexanoic acidHMDB
beta-LysineHMDB
beta-Lysine, (S)-isomerMeSH, HMDB
beta-Lysine, (R)-isomerMeSH, HMDB
(3S)-3,6-DiaminohexanoateChEBI
Molecular FormulaC6H14N2O2
Average Mass146.1876
Monoisotopic Mass146.105527702
IUPAC Name(3S)-3,6-diaminohexanoic acid
Traditional Name(3S)-3,6-diaminohexanoic acid
CAS Registry Number4299-56-3
SMILES
NCCC[C@H](N)CC(O)=O
InChI Identifier
InChI=1S/C6H14N2O2/c7-3-1-2-5(8)4-6(9)10/h5H,1-4,7-8H2,(H,9,10)/t5-/m0/s1
InChI KeyQKEWQOJCHPFEAF-YFKPBYRVSA-N