MiMeDB: Showing metabocard for O-Succinyl-L-homoserine (MMDBc0029648)

Plant

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:36:02 UTC

Update Date

2022-08-31 14:16:26 UTC

Metabolite ID

MMDBc0029648

Metabolite Identification

Common Name

O-Succinyl-L-homoserine

Description

O-succinyl-L-homoserine is a member of the chemical class known as Alpha Amino Acids and Derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).O-succinyl-L-homoserine is involved in bacterial transfulfuration pathway. Cystathionine gamma-synthase (CGS) is a pyridoxal phosphate-dependent enzyme that catalyzes a gamma-replacement reaction, in which the succinyl group of an O-succinyl-L-homoserine (L-OSHS) is displaced by the thiol of L-cysteine to form L-cystathionine, in the first step of the bacterial transsulfuration pathway. Cystathionine gamma-synthase (CGS) is a pyridoxal phosphate-dependent enzyme that catalyzes a gamma-replacement reaction, in which the succinyl group of an O-succinyl-L-homoserine (L-OSHS) is displaced by the thiol of L-cysteine to form L-cystathionine, in the first step of the bacterial transsulfuration pathway. (PMID 14503880 )

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1652303062005542D          

 15 14  0  0  1  0            999 V2000
   27.6994  -16.7679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.4149  -16.3531    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.6994  -17.5937    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.1341  -16.7640    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.8497  -16.3531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.5650  -16.7640    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   31.2843  -16.3492    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.5688  -17.5937    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   31.9998  -16.7640    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   31.2843  -15.6482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.9879  -16.3581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.2886  -16.7628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.5941  -16.3627    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8987  -16.7651    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5932  -15.5410    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  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  0  0  0  0
  6  8  1  1  0  0  0
  7  9  1  0  0  0  0
  7 10  2  0  0  0  0
  1 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029648

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C8H13NO6/c9-5(8(13)14)3-4-15-7(12)2-1-6(10)11/h5H,1-4,9H2,(H,10,11)(H,13,14)/t5-/m0/s1

> <INCHI_KEY>
GNISQJGXJIDKDJ-YFKPBYRVSA-N

> <FORMULA>
C8H13NO6

> <MOLECULAR_WEIGHT>
219.1919

> <EXACT_MASS>
219.074287153

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
28

> <JCHEM_AVERAGE_POLARIZABILITY>
20.513811131589183

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-2-amino-4-[(3-carboxypropanoyl)oxy]butanoic acid

> <ALOGPS_LOGP>
-3.31

> <JCHEM_LOGP>
-3.6100642791309556

> <ALOGPS_LOGS>
-1.40

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.112459497104107

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.688067433289202

> <JCHEM_PKA_STRONGEST_BASIC>
9.458196258009957

> <JCHEM_POLAR_SURFACE_AREA>
126.92000000000002

> <JCHEM_REFRACTIVITY>
46.95120000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.69e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
O-succinyl-L-homoserine

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0      51.706 -31.300   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      53.041 -30.526   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      51.706 -32.842   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      54.384 -31.293   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      55.719 -30.526   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      57.055 -31.293   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      58.397 -30.518   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0      57.062 -32.842   0.000  0.00  0.00           N+0
HETATM    9  O   UNK     0      59.733 -31.293   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      58.397 -29.210   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      50.377 -30.535   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      49.072 -31.291   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      47.776 -30.544   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      46.478 -31.295   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      47.774 -29.010   0.000  0.00  0.00           O+0
CONECT    1    2    3   11                                                  
CONECT    2    1    4                                                       
CONECT    3    1                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6    9   10                                                  
CONECT    8    6                                                            
CONECT    9    7                                                            
CONECT   10    7                                                            
CONECT   11    1   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
O-Succinylhomoserine	ChEBI
O4-Succinyl-L-homoserine	ChEBI
O-Succinylhomoserine, (DL)-isomer	MeSH

Molecular Formula

C₈H₁₃NO₆

Average Mass

219.1919

Monoisotopic Mass

219.074287153

IUPAC Name

(2S)-2-amino-4-[(3-carboxypropanoyl)oxy]butanoic acid

Traditional Name

O-succinyl-L-homoserine

CAS Registry Number

1492-23-5

SMILES

N[C@@H](CCOC(=O)CCC(O)=O)C(O)=O

InChI Identifier

InChI=1S/C8H13NO6/c9-5(8(13)14)3-4-15-7(12)2-1-6(10)11/h5H,1-4,9H2,(H,10,11)(H,13,14)/t5-/m0/s1

InChI Key

GNISQJGXJIDKDJ-YFKPBYRVSA-N

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
Tricarboxylic acid or derivatives
Fatty acid ester
Fatty acyl
Carboxylic acid ester
Amino acid
Carboxylic acid
Amine
Hydrocarbon derivative
Organic oxide
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Carbonyl group
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

o-succinylhomoserine (CHEBI:16160 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	8.69 g/L	ALOGPS
logP	-3.3	ALOGPS
logP	-3.6	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.69	ChemAxon
pKa (Strongest Basic)	9.46	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	126.92 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	46.95 m³·mol⁻¹	ChemAxon
Polarizability	20.51 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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	Proteobacteria	358	Human feces; Human sputum; Human ; Human pleural fluid plaque; Human feces; pleural fluid plaque; bal; Pig ; Human dental plaque; Human nasal swab; Human unknown; River trout ; Turkey	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	321	Human feces; Human pleural fluid plaque; Pig ; Human	Metabolic reconstruction
Bacteria	Actinobacteria	113	Human feces; Human ; Human pleural fluid plaque; Human dental plaque; Human sputum; Cattle	Metabolic reconstruction
Bacteria	Bacteroidetes	97	Human feces; Human ; Human appendix biopsy	Metabolic reconstruction
Bacteria	Fusobacteria	9	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Bacteria/NULL	Proteobacteria	1	Human feces; Human sputum; Human ; Human pleural fluid plaque; Human feces; pleural fluid plaque; bal; Pig ; Human dental plaque; Human nasal swab; Human unknown; River trout ; Turkey	Unknown; Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	4	Human feces	Unknown
Bacteria	Chloroflexi	1

Exposure Sources

Food Exposures

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

O-SUCCINYL-L-HOMOSERINE

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439406

PDB ID

Not Available

ChEBI ID

16160

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 ]
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 O-Succinyl-L-homoserine (MMDBc0029648)

MOL for #<Metabolite:0x0000560be29122a8>

3D MOL for #<Metabolite:0x0000560be29122a8>

3D SDF for #<Metabolite:0x0000560be29122a8>

3D-SDF for #<Metabolite:0x0000560be29122a8>

PDB for #<Metabolite:0x0000560be29122a8>

3D PDB for #<Metabolite:0x0000560be29122a8>

SMILES for #<Metabolite:0x0000560be29122a8>

INCHI for #<Metabolite:0x0000560be29122a8>

Structure for #<Metabolite:0x0000560be29122a8>

3D Structure for #<Metabolite:0x0000560be29122a8>