MiMeDB: Showing metabocard for N2-succinyl-L-arginine (MMDBc0032113)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:02:57 UTC

Update Date

2022-08-31 18:30:38 UTC

Metabolite ID

MMDBc0032113

Metabolite Identification

Common Name

N2-succinyl-L-arginine

Description

N2-Succinyl-L-arginine belongs to the class of Amino Fatty Acids. These are fatty acids contaning an amine group. (inferred from compound structure)

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04081523112D          

 19 18  0  0  0  0            999 V2000
   -4.2868    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5723   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5723   -1.2375    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   -2.8578    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7144   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8578    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5723   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.5723   -1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.7144    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  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  8 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
M  CHG  3   3   1  15  -1  18  -1
M  END
> <DATABASE_ID>
MMDBc0032113

> <DATABASE_NAME>
MIME

> <SMILES>
NC(=[NH2+])NCCC[C@H](NC(=O)CCC([O-])=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H18N4O5/c11-10(12)13-5-1-2-6(9(18)19)14-7(15)3-4-8(16)17/h6H,1-5H2,(H,14,15)(H,16,17)(H,18,19)(H4,11,12,13)/p-1/t6-/m0/s1

> <INCHI_KEY>
UMOXFSXIFQOWTD-LURJTMIESA-M

> <FORMULA>
C10H17N4O5

> <MOLECULAR_WEIGHT>
273.27

> <EXACT_MASS>
273.120443243

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.396454730352623

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-5-{[amino(iminiumyl)methyl]amino}-2-(3-carboxylatopropanamido)pentanoate

> <ALOGPS_LOGP>
-0.20

> <JCHEM_LOGP>
-3.786204805904579

> <ALOGPS_LOGS>
-1.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.070605562408759

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.283396595922066

> <JCHEM_PKA_STRONGEST_BASIC>
12.145416350737964

> <JCHEM_POLAR_SURFACE_AREA>
173.0

> <JCHEM_REFRACTIVITY>
96.73440000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.75e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N(2)-succinyl-L-arginine

> <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  N   UNK     0      -8.002   0.000   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      -6.668  -0.770   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0      -6.668  -2.310   0.000  0.00  0.00           N+1
HETATM    4  N   UNK     0      -5.335   0.000   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      -4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  N   UNK     0       1.334  -0.770   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.002   0.000   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0       6.668  -2.310   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0      -1.334   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                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    8   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

Synonyms

Value	Source
N(2)-(3-Carboxylatopropionyl)-L-arginine	ChEBI
N(2)-(3-Carboxylatopropionyl)-L-arginine anion	ChEBI
N(2)-Succinyl-L-arginine	ChEBI

Molecular Formula

C₁₀H₁₇N₄O₅

Average Mass

273.27

Monoisotopic Mass

273.120443243

IUPAC Name

(2S)-5-{[amino(iminiumyl)methyl]amino}-2-(3-carboxylatopropanamido)pentanoate

Traditional Name

N(2)-succinyl-L-arginine

CAS Registry Number

Not Available

SMILES

NC(=[NH2+])NCCC[C@H](NC(=O)CCC([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C10H18N4O5/c11-10(12)13-5-1-2-6(9(18)19)14-7(15)3-4-8(16)17/h6H,1-5H2,(H,14,15)(H,16,17)(H,18,19)(H4,11,12,13)/p-1/t6-/m0/s1

InChI Key

UMOXFSXIFQOWTD-LURJTMIESA-M

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-l-alpha-amino acids. These are n-acylated 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

N-acyl-L-alpha-amino acids

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

N-acyl-L-alpha-amino acid anion (CHEBI:58241 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	17.5 g/L	ALOGPS
logP	-0.2	ALOGPS
logP	-3.8	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	3.28	ChemAxon
pKa (Strongest Basic)	12.15	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	173 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	96.73 m³·mol⁻¹	ChemAxon
Polarizability	26.4 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	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00di-2090000000-17ac42ad4b74952a74c1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-044i-4190000000-942edcdeb0bd591ae2a1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9000000000-aa5dd01d82e492af084f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-4090000000-ac40e7fcd03acf8002dc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-9170000000-dff64d5881d443f1974f	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-ae2e61423731b6c79167	2015-09-15	View Spectrum

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013399	L-Arginine	CoA	Arginine N-succinyltransferase	Transfer of succinyl moiety	RHEA	34755880
MMDBr0013892	Hydrogen Ion	Carbon dioxide	N-succinylarginine dihydrolase	Hydrolysis	RHEA	34755880
MMDBr0013893	Hydrogen Ion	Carbon dioxide	N-succinylarginine dihydrolase	Hydrolysis	RHEA	34755880
MMDBr0018131	L-Arginine	Hydrogen Ion	Arginine N-succinyltransferase	Transfer of succinyl moiety	PathBank	31602464
MMDBr0018132	Hydrogen Ion	Carbon dioxide	N-succinylarginine dihydrolase	Hydrolysis of bond	PathBank	31602464
MMDBr0036106	N2-succinyl-L-arginine	Succinic acid	Acylamidase	Hydrolysis	RHEA	34755880

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

Exposure Sources

Source Type	Source Sub-type	Species	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

25245674

PDB ID

Not Available

ChEBI ID

58241

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 ]
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 N2-succinyl-L-arginine (MMDBc0032113)

MOL for #<Metabolite:0x00007fa4e4c3bac8>

3D MOL for #<Metabolite:0x00007fa4e4c3bac8>

3D SDF for #<Metabolite:0x00007fa4e4c3bac8>

3D-SDF for #<Metabolite:0x00007fa4e4c3bac8>

PDB for #<Metabolite:0x00007fa4e4c3bac8>

3D PDB for #<Metabolite:0x00007fa4e4c3bac8>

SMILES for #<Metabolite:0x00007fa4e4c3bac8>

INCHI for #<Metabolite:0x00007fa4e4c3bac8>

Structure for #<Metabolite:0x00007fa4e4c3bac8>

3D Structure for #<Metabolite:0x00007fa4e4c3bac8>