MiMeDB: Showing metabocard for N(2)-succinyl-L-citrulline (MMDBc0054594)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:20:04 UTC

Update Date

2022-08-12 20:09:01 UTC

Metabolite ID

MMDBc0054594

Metabolite Identification

Common Name

N(2)-succinyl-L-citrulline

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006051508202D          
 
 19 18  0  0  1  0            999 V2000
   16.3134  -14.2219    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   16.3134  -13.3853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5604  -12.9670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0245  -12.9670    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8494  -13.3853    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1383  -12.9670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.1383  -12.1305    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4272  -13.3853    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9631  -15.0585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6742  -15.4768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3853  -15.0585    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.1383  -15.4768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8494  -15.0585    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5604  -15.4768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3134  -15.0585    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.0245  -15.4768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7356  -15.0585    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.0245  -16.3134    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.6742  -16.3134    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  9 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
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
 15  1  1  6  0  0  0
 10 19  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054594

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H17N3O6/c11-10(19)12-5-1-2-6(9(17)18)13-7(14)3-4-8(15)16/h6H,1-5H2,(H,13,14)(H,15,16)(H,17,18)(H3,11,12,19)/t6-/m0/s1

> <INCHI_KEY>
ZSZFGMMEPZVGMH-LURJTMIESA-N

> <FORMULA>
C10H17N3O6

> <MOLECULAR_WEIGHT>
275.261

> <EXACT_MASS>
275.111735279

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.550923421056034

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-5-(carbamoylamino)-2-(3-carboxypropanamido)pentanoic acid

> <ALOGPS_LOGP>
-1.32

> <JCHEM_LOGP>
-2.026170248666667

> <ALOGPS_LOGS>
-2.00

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.3484739267579275

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.525745820972906

> <JCHEM_PKA_STRONGEST_BASIC>
-1.536132338855471

> <JCHEM_POLAR_SURFACE_AREA>
158.82

> <JCHEM_REFRACTIVITY>
61.66610000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.74e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-succinyl-L-citrulline

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  N   UNK     0      30.452 -26.548   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      30.452 -24.986   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      29.046 -24.205   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      31.779 -24.205   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      27.719 -24.986   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      26.391 -24.205   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      26.391 -22.644   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      25.064 -24.986   0.000  0.00  0.00           O+0
HETATM    9  N   UNK     0      22.331 -28.109   0.000  0.00  0.00           N+0
HETATM   10  C   UNK     0      23.659 -28.890   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      24.986 -28.109   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      26.391 -28.890   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      27.719 -28.109   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      29.046 -28.890   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      30.452 -28.109   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      31.779 -28.890   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      33.106 -28.109   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      31.779 -30.452   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      23.659 -30.452   0.000  0.00  0.00           O+0
CONECT    1    2   15                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9   10                                                            
CONECT   10    9   11   19                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16    1                                                  
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   10                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

Synonyms

Value	Source
N-Succinyl-L-citrulline	ChEBI
N(5)-Carbamoyl-N(2)-(3-carboxypropanoyl)-L-ornithine	ChEBI

Molecular Formula

C₁₀H₁₇N₃O₆

Average Mass

275.261

Monoisotopic Mass

275.111735279

IUPAC Name

(2S)-5-(carbamoylamino)-2-(3-carboxypropanamido)pentanoic acid

Traditional Name

N-succinyl-L-citrulline

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C10H17N3O6/c11-10(19)12-5-1-2-6(9(17)18)13-7(14)3-4-8(15)16/h6H,1-5H2,(H,13,14)(H,15,16)(H,17,18)(H3,11,12,19)/t6-/m0/s1

InChI Key

ZSZFGMMEPZVGMH-LURJTMIESA-N

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
Carboxamide group
Carbonic acid derivative
Secondary carboxylic acid amide
Urea
Carboxylic acid
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

N2-acyl-L-ornithine (CHEBI:51309 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.74 g/L	ALOGPS
logP	-1.3	ALOGPS
logP	-2	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	3.53	ChemAxon
pKa (Strongest Basic)	-1.5	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	158.82 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	61.67 m³·mol⁻¹	ChemAxon
Polarizability	26.55 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 GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0arr-0290000000-e0539837a4d2798fcca6	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00lr-2960000000-347192278254fbe4a792	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-00xr-7900000000-7c31faba606c531fe9e6	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-008c-3190000000-6f3374593e8fcd0ca29a	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06s6-5590000000-c34fb19d74b1348f95f9	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9100000000-bab3dff349e14305bc22	2019-02-23	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

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	Bacteroidetes	2	Human feces; Human

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

C18048

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25137932

PDB ID

Not Available

ChEBI ID

51309

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 N(2)-succinyl-L-citrulline (MMDBc0054594)

MOL for #<Metabolite:0x00007fecf5310828>

3D MOL for #<Metabolite:0x00007fecf5310828>

3D SDF for #<Metabolite:0x00007fecf5310828>

3D-SDF for #<Metabolite:0x00007fecf5310828>

PDB for #<Metabolite:0x00007fecf5310828>

3D PDB for #<Metabolite:0x00007fecf5310828>

SMILES for #<Metabolite:0x00007fecf5310828>

INCHI for #<Metabolite:0x00007fecf5310828>

Structure for #<Metabolite:0x00007fecf5310828>

3D Structure for #<Metabolite:0x00007fecf5310828>