MiMeDB: Showing metabocard for N2-succinylglutamate (MMDBc0032114)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:02:59 UTC

Update Date

2022-08-31 18:30:39 UTC

Metabolite ID

MMDBc0032114

Metabolite Identification

Common Name

N2-succinylglutamate

Description

N2-succinylglutamate is an intermediate in L-arginine degradation II pathway in E.coli. It is a product for the enzyme succinylglutamate desuccinylase which catalyzes the reaction N2-succinyl-L-glutamate 5-semialdehyde + NAD+ + H2O -> N2-succinylglutamate + NADH + 2 H+. It is also the substrate for the enzyme succinylglutamate semialdehyde dehydrogenase which catalyzes the reaction N2-succinylglutamate + H2O -> succinate + L-glutamate (BioCyc: N2-SUCCINYLGLUTAMATE).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04081523132D          

 17 16  0  0  0  0            999 V2000
   -3.5723    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.8578   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8578   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8578   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.8578   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4289    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  2  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
M  CHG  3   1  -1  13  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0032114

> <DATABASE_NAME>
MIME

> <SMILES>
[O-]C(=O)CC[C@H](NC(=O)CCC([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13NO7/c11-6(2-4-8(14)15)10-5(9(16)17)1-3-7(12)13/h5H,1-4H2,(H,10,11)(H,12,13)(H,14,15)(H,16,17)/p-3/t5-/m0/s1

> <INCHI_KEY>
JCNBNOQGFSXOML-YFKPBYRVSA-K

> <FORMULA>
C9H10NO7

> <MOLECULAR_WEIGHT>
244.181

> <EXACT_MASS>
244.047372406

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.05996899406932

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-(3-carboxylatopropanamido)pentanedioate

> <ALOGPS_LOGP>
-0.50

> <JCHEM_LOGP>
-1.288152669666667

> <ALOGPS_LOGS>
-0.89

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.7807922229565585

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.145285433595691

> <JCHEM_PKA_STRONGEST_BASIC>
-1.9877795392341007

> <JCHEM_POLAR_SURFACE_AREA>
149.48999999999998

> <JCHEM_REFRACTIVITY>
84.1361

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.82e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-succinyl-L-glutamate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-APR-15         0                                  
HETATM    1  O   UNK     0      -6.668   0.000   0.000  0.00  0.00           O-1
HETATM    2  C   UNK     0      -5.335  -0.770   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      -5.335  -2.310   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -4.001   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       0.000  -0.770   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0       1.334   0.000   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       1.334   1.540   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.667  -0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335  -0.770   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       6.668   0.000   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       5.335  -2.310   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334   1.540   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       0.000   2.310   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      -2.667   2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12                                                            
CONECT   15    6   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   32    0
END

Synonyms

Value	Source
N-Succinyl-L-glutamate	ChEBI
N-Succinyl-L-glutamic acid	Generator
N2-Succinylglutamic acid	Generator
N(2)-Succinylglutamate	MeSH

Molecular Formula

C₉H₁₀NO₇

Average Mass

244.181

Monoisotopic Mass

244.047372406

IUPAC Name

(2S)-2-(3-carboxylatopropanamido)pentanedioate

Traditional Name

N-succinyl-L-glutamate

CAS Registry Number

Not Available

SMILES

[O-]C(=O)CC[C@H](NC(=O)CCC([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C9H13NO7/c11-6(2-4-8(14)15)10-5(9(16)17)1-3-7(12)13/h5H,1-4H2,(H,10,11)(H,12,13)(H,14,15)(H,16,17)/p-3/t5-/m0/s1

InChI Key

JCNBNOQGFSXOML-YFKPBYRVSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glutamic acid and derivatives. Glutamic acid and derivatives are compounds containing glutamic acid or a derivative thereof resulting from reaction of glutamic acid at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Glutamic acid and derivatives

Alternative Parents

Substituents

Glutamic acid or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
N-acyl-l-alpha-amino acid
Tricarboxylic acid or derivatives
Fatty amide
N-acyl-amine
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Carboxylic acid
Carbonyl group
Organooxygen compound
Organonitrogen compound
Organic oxide
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tricarboxylic acid trianion (CHEBI:58763 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	38.2 g/L	ALOGPS
logP	-0.5	ALOGPS
logP	-1.3	ChemAxon
logS	-0.89	ALOGPS
pKa (Strongest Acidic)	3.15	ChemAxon
pKa (Strongest Basic)	-2	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	149.49 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	84.14 m³·mol⁻¹	ChemAxon
Polarizability	21.06 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

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

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018134	N2-Succinyl-L-glutamic acid 5-semialdehyde	N2-succinylglutamate	N-succinylglutamate 5-semialdehyde dehydrogenase	Dehydrogenation	PathBank	31602464
MMDBr0018135	N2-succinylglutamate	L-Glutamic acid	Succinylglutamate desuccinylase	Hydrolysis of carbon-nitrogen bond	PathBank	31602464

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	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25244383

PDB ID

Not Available

ChEBI ID

58763

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]

Showing metabocard for N2-succinylglutamate (MMDBc0032114)

MOL for #<Metabolite:0x00007f923027f028>

3D MOL for #<Metabolite:0x00007f923027f028>

3D SDF for #<Metabolite:0x00007f923027f028>

3D-SDF for #<Metabolite:0x00007f923027f028>

PDB for #<Metabolite:0x00007f923027f028>

3D PDB for #<Metabolite:0x00007f923027f028>

SMILES for #<Metabolite:0x00007f923027f028>

INCHI for #<Metabolite:0x00007f923027f028>

Structure for #<Metabolite:0x00007f923027f028>

3D Structure for #<Metabolite:0x00007f923027f028>