MiMeDB: Showing metabocard for N(5)-[(S)-citryl]-D-ornithine (MMDBc0056186)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:18:58 UTC

Update Date

2025-10-07 16:09:38 UTC

Metabolite ID

MMDBc0056186

Metabolite Identification

Common Name

N(5)-[(S)-citryl]-D-ornithine

Description

N(5)-[(S)-citryl]-D-ornithine is a non-proteinogenic amino acid derivative belonging to the class of ornithine-based metabolites. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and potential applications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222182D          

 22 21  0  0  1  0            999 V2000
    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
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243   -1.7605    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.3493   -1.7605    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118   -1.0461    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4618   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  1  0  0  0  0
  6  2  1  0  0  0  0
  7  4  1  0  0  0  0
  8  5  1  0  0  0  0
  9  6  1  0  0  0  0
 11  4  1  6  0  0  0
 11  5  1  0  0  0  0
 11 10  1  0  0  0  0
  6 12  1  6  0  0  0
 13  3  1  4  0  0  0
 13  7  2  0  0  0  0
 14  7  1  0  0  0  0
 15  8  2  0  0  0  0
 16  8  1  0  0  0  0
 17  9  2  0  0  0  0
 18  9  1  0  0  0  0
 19 10  2  0  0  0  0
 20 10  1  0  0  0  0
 11 21  1  1  0  0  0
  6 22  1  6  0  0  0
M  CHG  2  14  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0056186

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](N)(CCCN=C([O-])C[C@](O)(CC([O-])=O)C(O)=O)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N2O8/c12-6(9(17)18)2-1-3-13-7(14)4-11(21,10(19)20)5-8(15)16/h6,21H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/p-2/t6-,11+/m1/s1

> <INCHI_KEY>
FFFKYGCGRTUBJH-KBUNVGBDSA-L

> <FORMULA>
C11H16N2O8

> <MOLECULAR_WEIGHT>
304.256

> <EXACT_MASS>
304.091762643

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
37

> <JCHEM_AVERAGE_POLARIZABILITY>
27.68521182563258

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S)-4-{[(4R)-4-amino-4-carboxybutyl]-C-hydroxycarbonimidoyl}-3-carboxy-3-hydroxybutanoate

> <JCHEM_LOGP>
-5.566871659844997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1077579786877143

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7766773939845901

> <JCHEM_PKA_STRONGEST_BASIC>
9.526276180554994

> <JCHEM_POLAR_SURFACE_AREA>
196.39999999999995

> <JCHEM_REFRACTIVITY>
87.54159999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-4-{[(4R)-4-amino-4-carboxybutyl]-C-hydroxycarbonimidoyl}-3-carboxy-3-hydroxybutanoate

> <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       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002  -3.080   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.542  -4.620   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      10.312  -3.286   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.002  -6.160   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.002  -4.620   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       1.334  -2.310   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       6.668  -0.770   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0       5.335  -3.080   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0      11.852  -3.286   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       9.542  -1.953   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       9.336  -6.930   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       6.668  -6.930   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0       6.462  -4.620   0.000  0.00  0.00           O+0
HETATM   22  H   UNK     0       1.334   0.770   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1   13                                                       
CONECT    4    7   11                                                       
CONECT    5    8   11                                                       
CONECT    6    2    9   12   22                                             
CONECT    7    4   13   14                                                  
CONECT    8    5   15   16                                                  
CONECT    9    6   17   18                                                  
CONECT   10   11   19   20                                                  
CONECT   11    4    5   10   21                                             
CONECT   12    6                                                            
CONECT   13    3    7                                                       
CONECT   14    7                                                            
CONECT   15    8                                                            
CONECT   16    8                                                            
CONECT   17    9                                                            
CONECT   18    9                                                            
CONECT   19   10                                                            
CONECT   20   10                                                            
CONECT   21   11                                                            
CONECT   22    6                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   42    0
END

Synonyms

Not Available

Molecular Formula

C₁₁H₁₆N₂O₈

Average Mass

304.256

Monoisotopic Mass

304.091762643

IUPAC Name

(3S)-4-{[(4R)-4-amino-4-carboxybutyl]-C-hydroxycarbonimidoyl}-3-carboxy-3-hydroxybutanoate

Traditional Name

(3S)-4-{[(4R)-4-amino-4-carboxybutyl]-C-hydroxycarbonimidoyl}-3-carboxy-3-hydroxybutanoate

CAS Registry Number

Not Available

SMILES

[H][C@@](N)(CCCN=C([O-])C[C@](O)(CC([O-])=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C11H18N2O8/c12-6(9(17)18)2-1-3-13-7(14)4-11(21,10(19)20)5-8(15)16/h6,21H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/p-2/t6-,11+/m1/s1

InChI Key

FFFKYGCGRTUBJH-KBUNVGBDSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-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

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Tricarboxylic acid or derivatives
Hydroxy acid
Alpha-hydroxy acid
Tertiary alcohol
Amino acid
Carboxylic acid
Carboximidic acid derivative
Carboximidic acid
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Primary aliphatic amine
Carbonyl group
Amine
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.6	ChemAxon
pKa (Strongest Acidic)	1.78	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	196.4 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	87.54 m³·mol⁻¹	ChemAxon
Polarizability	27.69 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

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	Firmicutes	1	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

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

145865169

PDB ID

Not Available

ChEBI ID

Not Available

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 N(5)-[(S)-citryl]-D-ornithine (MMDBc0056186)

MOL for #<Metabolite:0x0000561537e43c28>

3D MOL for #<Metabolite:0x0000561537e43c28>

3D SDF for #<Metabolite:0x0000561537e43c28>

3D-SDF for #<Metabolite:0x0000561537e43c28>

PDB for #<Metabolite:0x0000561537e43c28>

3D PDB for #<Metabolite:0x0000561537e43c28>

SMILES for #<Metabolite:0x0000561537e43c28>

INCHI for #<Metabolite:0x0000561537e43c28>

Structure for #<Metabolite:0x0000561537e43c28>

3D Structure for #<Metabolite:0x0000561537e43c28>