Showing metabocard for (3S,5S)-3,5-Diaminocaproate (MMDBc0049859)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:44:56 UTC
Update Date2025-01-15 22:39:31 UTC
Metabolite IDMMDBc0049859
Metabolite Identification
Common Name(3S,5S)-3,5-Diaminocaproate
Description3,5-diaminohexanoic acid,which requires a cobamide coenzyme for formation. , is readily fermented to volatile acids by extracts of Clostridium SB4. (3S,5S)-3,5-Diaminohexanoate is involved in the lysine degradation pathway. (3S,5S)-3,5-Diaminohexanoate is produced from (3S)-3,6-Diaminohexanoate through the action of beta-lysine 5,6-aminomutase [EC:5.4.3.3]. (3S,5S)-3,5-Diaminohexanoate is then converted into(S)-5-Amino-3-oxohexanoic acid.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00005645ca1b8940>


  Mrv0541 02241203392D          

 10  9  0  0  1  0            999 V2000
   17.6359  -10.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8733   -9.4408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.1107   -8.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4608  -10.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.6983   -9.4408    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.6983   -8.0122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8733  -10.8699    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.1107  -10.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.1107   -7.2977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8733   -8.0122    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  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
Download

3D MOL for #<Metabolite:0x00005645ca1b8940>

HMDB0012115
     RDKit          3D
(3S,5S)-3,5-Diaminohexanoate
 24 23  0  0  0  0  0  0  0  0999 V2000
   -2.4554   -0.6049   -0.1125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6444    0.6328    0.0751 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7043    1.4414   -1.0863 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2186    0.3922    0.4883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5609   -0.4145   -0.4905 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1179   -1.7159   -0.6176 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9470   -0.7202   -0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7987    0.4376    0.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9584    0.2055    0.6903 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4298    1.7588    0.0542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3070   -1.3608    0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5387   -0.2994   -0.0191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3577   -1.0810   -1.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1210    1.2142    0.9160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2077    2.3338   -1.0625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4836    1.3303   -1.7103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1909   -0.1745    1.4660 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2476    1.3661    0.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    0.0611   -1.4875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0587   -2.1323    0.3602 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5053   -2.3529   -1.1999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9391   -1.3978    0.8659 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4425   -1.3020   -0.8466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9225    2.3825   -0.5647 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  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
  1 13  1  0
  2 14  1  1
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  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:0x00005645ca1b8940>


  Mrv0541 02241203392D          

 10  9  0  0  1  0            999 V2000
   17.6359  -10.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8733   -9.4408    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.1107   -8.7262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4608  -10.1553    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.6983   -9.4408    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.6983   -8.0122    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.8733  -10.8699    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.1107  -10.1553    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.1107   -7.2977    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.8733   -8.0122    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  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>
MMDBc0049859

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C6H14N2O2/c1-4(7)2-5(8)3-6(9)10/h4-5H,2-3,7-8H2,1H3,(H,9,10)/t4-,5-/m0/s1

> <INCHI_KEY>
NGDLSXMSQYUVSJ-WHFBIAKZSA-N

> <FORMULA>
C6H14N2O2

> <MOLECULAR_WEIGHT>
146.1876

> <EXACT_MASS>
146.105527702

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
15.576979154372966

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,5S)-3,5-diaminohexanoic acid

> <ALOGPS_LOGP>
-3.53

> <JCHEM_LOGP>
-3.5349171218929025

> <ALOGPS_LOGS>
-0.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.248886209739101

> <JCHEM_PKA_STRONGEST_BASIC>
10.749562037886385

> <JCHEM_POLAR_SURFACE_AREA>
89.34

> <JCHEM_REFRACTIVITY>
37.607

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.26e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-erythro-3,5-diaminohexanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for #<Metabolite:0x00005645ca1b8940>

HMDB0012115
     RDKit          3D
(3S,5S)-3,5-Diaminohexanoate
 24 23  0  0  0  0  0  0  0  0999 V2000
   -2.4554   -0.6049   -0.1125 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6444    0.6328    0.0751 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7043    1.4414   -1.0863 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2186    0.3922    0.4883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5609   -0.4145   -0.4905 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1179   -1.7159   -0.6176 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.9470   -0.7202   -0.0146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7987    0.4376    0.2500 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9584    0.2055    0.6903 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4298    1.7588    0.0542 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3070   -1.3608    0.6842 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5387   -0.2994   -0.0191 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3577   -1.0810   -1.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1210    1.2142    0.9160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2077    2.3338   -1.0625 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4836    1.3303   -1.7103 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1909   -0.1745    1.4660 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2476    1.3661    0.7159 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6542    0.0611   -1.4875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0587   -2.1323    0.3602 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5053   -2.3529   -1.1999 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9391   -1.3978    0.8659 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4425   -1.3020   -0.8466 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9225    2.3825   -0.5647 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  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
  1 13  1  0
  2 14  1  1
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  6
  6 20  1  0
  6 21  1  0
  7 22  1  0
  7 23  1  0
 10 24  1  0
M  END
Download

PDB for #<Metabolite:0x00005645ca1b8940>

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      32.920 -18.957   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      35.230 -17.623   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      37.540 -16.289   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      34.460 -18.957   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      36.770 -17.623   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      36.770 -14.956   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      35.230 -20.290   0.000  0.00  0.00           N+0
HETATM    8  N   UNK     0      37.540 -18.957   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      37.540 -13.622   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      35.230 -14.956   0.000  0.00  0.00           O+0
CONECT    1    4                                                            
CONECT    2    4    5                                                       
CONECT    3    5    6                                                       
CONECT    4    1    2    7                                                  
CONECT    5    2    3    8                                                  
CONECT    6    3    9   10                                                  
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9    6                                                            
CONECT   10    6                                                            
MASTER        0    0    0    0    0    0    0    0   10    0   18    0
END
Download

3D PDB for #<Metabolite:0x00005645ca1b8940>

COMPND    HMDB0012115
HETATM    1  C1  UNL     1      -2.455  -0.605  -0.113  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.644   0.633   0.075  1.00  0.00           C  
HETATM    3  N1  UNL     1      -1.704   1.441  -1.086  1.00  0.00           N  
HETATM    4  C3  UNL     1      -0.219   0.392   0.488  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.561  -0.415  -0.490  1.00  0.00           C  
HETATM    6  N2  UNL     1      -0.118  -1.716  -0.618  1.00  0.00           N  
HETATM    7  C5  UNL     1       1.947  -0.720  -0.015  1.00  0.00           C  
HETATM    8  C6  UNL     1       2.799   0.438   0.250  1.00  0.00           C  
HETATM    9  O1  UNL     1       3.958   0.206   0.690  1.00  0.00           O  
HETATM   10  O2  UNL     1       2.430   1.759   0.054  1.00  0.00           O  
HETATM   11  H1  UNL     1      -2.307  -1.361   0.684  1.00  0.00           H  
HETATM   12  H2  UNL     1      -3.539  -0.299  -0.019  1.00  0.00           H  
HETATM   13  H3  UNL     1      -2.358  -1.081  -1.097  1.00  0.00           H  
HETATM   14  H4  UNL     1      -2.121   1.214   0.916  1.00  0.00           H  
HETATM   15  H5  UNL     1      -1.208   2.334  -1.063  1.00  0.00           H  
HETATM   16  H6  UNL     1      -2.484   1.330  -1.710  1.00  0.00           H  
HETATM   17  H7  UNL     1      -0.191  -0.175   1.466  1.00  0.00           H  
HETATM   18  H8  UNL     1       0.248   1.366   0.716  1.00  0.00           H  
HETATM   19  H9  UNL     1       0.654   0.061  -1.488  1.00  0.00           H  
HETATM   20  H10 UNL     1      -0.059  -2.132   0.360  1.00  0.00           H  
HETATM   21  H11 UNL     1       0.505  -2.353  -1.200  1.00  0.00           H  
HETATM   22  H12 UNL     1       1.939  -1.398   0.866  1.00  0.00           H  
HETATM   23  H13 UNL     1       2.443  -1.302  -0.847  1.00  0.00           H  
HETATM   24  H14 UNL     1       2.923   2.382  -0.565  1.00  0.00           H  
CONECT    1    2   11   12   13
CONECT    2    3    4   14
CONECT    3   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
Download

SMILES for #<Metabolite:0x00005645ca1b8940>

C[C@H](N)C[C@H](N)CC(O)=O
Download

INCHI for #<Metabolite:0x00005645ca1b8940>

InChI=1S/C6H14N2O2/c1-4(7)2-5(8)3-6(9)10/h4-5H,2-3,7-8H2,1H3,(H,9,10)/t4-,5-/m0/s1
Download
Synonyms
ValueSource
(3S,5S)-3,5-Diaminocaproic acidChEBI
L-Erythro-3,5-diaminohexanoic acidChEBI
L-Erythro-3,5-diaminohexanoateKegg
(3S,5S)-3,5-DiaminocaproateKegg
L-Erythro-3,5-diaminocaproateKegg
L-Erythro-3,5-diaminocaproic acidGenerator
(3S,5S)-3,5-Diaminohexanoic acidGenerator
3,5-diamino-HexanoateHMDB
3,5-diamino-Hexanoic acidHMDB
3,5-DiaminohexanoateHMDB
3,5-Diaminohexanoic acidHMDB
(3S,5S)-3,5-DiaminohexanoateGenerator
3,5-Diaminohexanoate dihydrochlorideMeSH, HMDB
Molecular FormulaC6H14N2O2
Average Mass146.1876
Monoisotopic Mass146.105527702
IUPAC Name(3S,5S)-3,5-diaminohexanoic acid
Traditional NameL-erythro-3,5-diaminohexanoate
CAS Registry NumberNot Available
SMILES
C[C@H](N)C[C@H](N)CC(O)=O
InChI Identifier
InChI=1S/C6H14N2O2/c1-4(7)2-5(8)3-6(9)10/h4-5H,2-3,7-8H2,1H3,(H,9,10)/t4-,5-/m0/s1
InChI KeyNGDLSXMSQYUVSJ-WHFBIAKZSA-N