Showing metabocard for carboxynorspermidine (MMDBc0055787)

Record Information
Version2.0
StatusDetected and Quantified
Creation Date2022-06-17 20:06:31 UTC
Update Date2025-10-07 16:09:21 UTC
Metabolite IDMMDBc0055787
Metabolite Identification
Common Namecarboxynorspermidine
DescriptionCarboxynorspermidine is a polyamine metabolite belonging to the chemical class of diamines. Its chemical structure features a carboxyl group attached to the norspermidine backbone, which is synthesized through a specific biosynthetic pathway starting from aspartate β-semialdehyde. This pathway involves the conversion of aspartate β-semialdehyde to 1,3-diaminopropane, leading to the formation of norspermidine via carboxynorspermidine as an intermediate (PMID:39230569 ). Carboxynorspermidine plays a role in various biological processes, including the regulation of biofilm formation in Vibrio cholerae, where norspermidine, synthesized by carboxynorspermidine decarboxylase (NspC), is a key player (PMID:22239666 ). Additionally, the enzyme carboxynorspermidine decarboxylase is crucial for synthesizing spermidine in Campylobacter jejuni, highlighting its importance in polyamine metabolism (PMID:22025614 ). The enzymatic activity of carboxynorspermidine decarboxylase and carboxynorspermidine dehydrogenase has been characterized through X-ray structure determination, revealing insights into their substrate specificity (PMID:20534592 ). Overall, carboxynorspermidine is integral to polyamine biosynthesis and is associated with various enzymatic pathways in bacteria.
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007faddc4b7490>


  Mrv1652306172222062D          

 13 12  0  0  1  0            999 V2000
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0493    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6664    0.7145    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.3349    1.9520    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0493   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  2  1  0  0  0  0
  7  6  1  0  0  0  0
  8  3  1  0  0  0  0
  6  9  1  1  0  0  0
 10  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
  6 13  1  1  0  0  0
M  CHG  2   8   1   9   1
M  END
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3D MOL for #<Metabolite:0x00007faddc4b7490>

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3D SDF for #<Metabolite:0x00007faddc4b7490>

  Mrv1652306172222062D          

 13 12  0  0  1  0            999 V2000
   -1.2375    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6204    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9520    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9059    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    1.1270    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.0493    0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6664    0.7145    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    2.3349    1.9520    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.1914    0.7145    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7638    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0493   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3349    0.3020    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  2  1  0  0  0  0
  7  6  1  0  0  0  0
  8  3  1  0  0  0  0
  6  9  1  1  0  0  0
 10  4  1  0  0  0  0
 10  5  1  0  0  0  0
 11  7  2  0  0  0  0
 12  7  1  0  0  0  0
  6 13  1  1  0  0  0
M  CHG  2   8   1   9   1
M  END
> <DATABASE_ID>
MMDBc0055787

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]([NH3+])(CCNCCC[NH3+])C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H17N3O2/c8-3-1-4-10-5-2-6(9)7(11)12/h6,10H,1-5,8-9H2,(H,11,12)/p+2/t6-/m0/s1

> <INCHI_KEY>
KFJYMJZJSUORBX-LURJTMIESA-P

> <FORMULA>
C7H19N3O2

> <MOLECULAR_WEIGHT>
177.247

> <EXACT_MASS>
177.146629704

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
20.29719297445432

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S)-3-[(3-azaniumylpropyl)amino]-1-carboxypropan-1-aminium

> <JCHEM_LOGP>
-4.520832739125558

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.7121613610870448

> <JCHEM_PKA_STRONGEST_BASIC>
10.328427793345238

> <JCHEM_POLAR_SURFACE_AREA>
104.61

> <JCHEM_REFRACTIVITY>
68.73929999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-3-[(3-ammoniopropyl)amino]-1-carboxypropan-1-aminium

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007faddc4b7490>
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PDB for #<Metabolite:0x00007faddc4b7490>
HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -2.310   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.025   1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.644   2.104   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.976   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.691   2.104   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.358   2.104   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.692   1.334   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      -4.977   1.334   0.000  0.00  0.00           N+1
HETATM    9  N   UNK     0       4.358   3.644   0.000  0.00  0.00           N+1
HETATM   10  N   UNK     0       0.357   1.334   0.000  0.00  0.00           N+0
HETATM   11  O   UNK     0       7.026   2.104   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.692  -0.206   0.000  0.00  0.00           O+0
HETATM   13  H   UNK     0       4.358   0.564   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    5    6                                                       
CONECT    3    1    8                                                       
CONECT    4    1   10                                                       
CONECT    5    2   10                                                       
CONECT    6    2    7    9   13                                             
CONECT    7    6   11   12                                                  
CONECT    8    3                                                            
CONECT    9    6                                                            
CONECT   10    4    5                                                       
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    6                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

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3D PDB for #<Metabolite:0x00007faddc4b7490>
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SMILES for #<Metabolite:0x00007faddc4b7490>
[H][C@]([NH3+])(CCNCCC[NH3+])C(O)=O
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INCHI for #<Metabolite:0x00007faddc4b7490>
InChI=1S/C7H17N3O2/c8-3-1-4-10-5-2-6(9)7(11)12/h6,10H,1-5,8-9H2,(H,11,12)/p+2/t6-/m0/s1
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Synonyms
ValueSource
(2S)-2-Ammonio-4-[(3-ammoniopropyl)ammonio]butanoateChEBI
CarboxynorspermidineChEBI
(2S)-2-Ammonio-4-[(3-ammoniopropyl)ammonio]butanoic acidGenerator
Molecular FormulaC7H19N3O2
Average Mass177.247
Monoisotopic Mass177.146629704
IUPAC Name(1S)-3-[(3-azaniumylpropyl)amino]-1-carboxypropan-1-aminium
Traditional Name(1S)-3-[(3-ammoniopropyl)amino]-1-carboxypropan-1-aminium
CAS Registry NumberNot Available
SMILES
[H][C@]([NH3+])(CCNCCC[NH3+])C(O)=O
InChI Identifier
InChI=1S/C7H17N3O2/c8-3-1-4-10-5-2-6(9)7(11)12/h6,10H,1-5,8-9H2,(H,11,12)/p+2/t6-/m0/s1
InChI KeyKFJYMJZJSUORBX-LURJTMIESA-P