MiMeDB: Showing metabocard for carboxyspermidine (MMDBc0055788)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:06:32 UTC

Update Date

2025-10-07 16:09:21 UTC

Metabolite ID

MMDBc0055788

Metabolite Identification

Common Name

carboxyspermidine

Description

Carboxyspermidine is a polyamine metabolite involved in the biosynthesis of spermidine, classified within the chemical class of polyamines. Its chemical structure features a carbon chain with multiple amine groups, which are crucial for its biological functions. Carboxyspermidine plays a significant role in alternative polyamine biosynthetic pathways, particularly in certain bacteria, where it is produced from putrescine through the action of carboxyspermidine dehydrogenase (CASDH) and carboxyspermidine decarboxylase (CASDC). These enzymes facilitate the conversion of putrescine into spermidine, with CASDH being primarily responsible for the production of spermidine from carboxyspermidine (PMID:40074085 ). In various human gut microbes, including Helicobacter pylori and Campylobacter jejuni, this alternative pathway is utilized instead of the classical route commonly found in eukaryotes (PMID:36283333 ). The metabolic pathway involving carboxyspermidine also includes the sequential conversion from arginine to agmatine, then to putrescine, and finally to carboxyspermidine (PMID:37314369 ). Overall, carboxyspermidine is a critical intermediate in polyamine metabolism, influencing cellular functions and growth in various microbial species.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222062D          

 14 13  0  0  1  0            999 V2000
    7.4763   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7618   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9039   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.1908   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0474   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6184   -1.8414    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.8414    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9052   -1.8414    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.1895   -2.6664    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    5.3329   -1.4289    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.7605   -1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.6039    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1895   -1.0164    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  3  1  0  0  0  0
  7  3  1  0  0  0  0
  8  7  1  0  0  0  0
  9  4  1  0  0  0  0
  7 10  1  1  0  0  0
 11  5  1  0  0  0  0
 11  6  1  0  0  0  0
 12  8  2  0  0  0  0
 13  8  1  0  0  0  0
  7 14  1  1  0  0  0
M  CHG  2   9   1  10   1
M  END
> <DATABASE_ID>
MMDBc0055788

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H19N3O2/c9-4-1-2-5-11-6-3-7(10)8(12)13/h7,11H,1-6,9-10H2,(H,12,13)/p+2/t7-/m0/s1

> <INCHI_KEY>
ICLFWLHIBPQMFT-ZETCQYMHSA-P

> <FORMULA>
C8H21N3O2

> <MOLECULAR_WEIGHT>
191.274

> <EXACT_MASS>
191.162279768

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
34

> <JCHEM_AVERAGE_POLARIZABILITY>
22.140889778260505

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S)-3-[(4-azaniumylbutyl)amino]-1-carboxypropan-1-aminium

> <JCHEM_LOGP>
-4.183638278510696

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5724714480750484

> <JCHEM_PKA_STRONGEST_BASIC>
10.662168473439076

> <JCHEM_POLAR_SURFACE_AREA>
104.61

> <JCHEM_REFRACTIVITY>
73.38389999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1S)-3-[(4-ammoniobutyl)amino]-1-carboxypropan-1-aminium

> <JCHEM_VEBER_RULE>
0

$$$$

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      13.956  -3.437   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.622  -2.667   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.287  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.289  -2.667   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      11.288  -3.437   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.621  -3.437   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.954  -3.437   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0      16.623  -3.437   0.000  0.00  0.00           N+1
HETATM   10  N   UNK     0       5.954  -4.977   0.000  0.00  0.00           N+1
HETATM   11  N   UNK     0       9.955  -2.667   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       3.286  -3.437   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.620  -1.127   0.000  0.00  0.00           O+0
HETATM   14  H   UNK     0       5.954  -1.897   0.000  0.00  0.00           H+0
CONECT    1    2    4                                                       
CONECT    2    1    5                                                       
CONECT    3    6    7                                                       
CONECT    4    1    9                                                       
CONECT    5    2   11                                                       
CONECT    6    3   11                                                       
CONECT    7    3    8   10   14                                             
CONECT    8    7   12   13                                                  
CONECT    9    4                                                            
CONECT   10    7                                                            
CONECT   11    5    6                                                       
CONECT   12    8                                                            
CONECT   13    8                                                            
CONECT   14    7                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
(2S)-2-Ammonio-5-[(3-ammoniopropyl)ammonio]pentanoate	ChEBI
Carboxyspermidine	ChEBI
(2S)-2-Ammonio-5-[(3-ammoniopropyl)ammonio]pentanoic acid	Generator

Molecular Formula

C₈H₂₁N₃O₂

Average Mass

191.274

Monoisotopic Mass

191.162279768

IUPAC Name

(1S)-3-[(4-azaniumylbutyl)amino]-1-carboxypropan-1-aminium

Traditional Name

(1S)-3-[(4-ammoniobutyl)amino]-1-carboxypropan-1-aminium

CAS Registry Number

Not Available

SMILES

[H][C@]([NH3+])(CCNCCCC[NH3+])C(O)=O

InChI Identifier

InChI=1S/C8H19N3O2/c9-4-1-2-5-11-6-3-7(10)8(12)13/h7,11H,1-6,9-10H2,(H,12,13)/p+2/t7-/m0/s1

InChI Key

ICLFWLHIBPQMFT-ZETCQYMHSA-P

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as l-alpha-amino acids. These are alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

L-alpha-amino acids

Alternative Parents

Substituents

L-alpha-amino acid
Fatty acid
Carboxylic acid salt
Amino acid
Carboxylic acid
Secondary aliphatic amine
Monocarboxylic acid or derivatives
Secondary amine
Organic salt
Organic nitrogen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Carbonyl group
Primary aliphatic amine
Amine
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Organic cation
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

alpha-amino-acid cation (CHEBI:65072 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.2	ChemAxon
pKa (Strongest Acidic)	2.57	ChemAxon
pKa (Strongest Basic)	10.66	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	104.61 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	73.38 m³·mol⁻¹	ChemAxon
Polarizability	22.14 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-20	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Proteobacteria	4	Human
Bacteria	Proteobacteria	3	Human

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

28532801

KEGG Compound ID

Not Available

BioCyc ID

CPD-10012

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70678730

PDB ID

Not Available

ChEBI ID

65072

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for carboxyspermidine (MMDBc0055788)

MOL for #<Metabolite:0x00007fadd843ae08>

3D MOL for #<Metabolite:0x00007fadd843ae08>

3D SDF for #<Metabolite:0x00007fadd843ae08>

3D-SDF for #<Metabolite:0x00007fadd843ae08>

PDB for #<Metabolite:0x00007fadd843ae08>

3D PDB for #<Metabolite:0x00007fadd843ae08>

SMILES for #<Metabolite:0x00007fadd843ae08>

INCHI for #<Metabolite:0x00007fadd843ae08>

Structure for #<Metabolite:0x00007fadd843ae08>

3D Structure for #<Metabolite:0x00007fadd843ae08>