MiMeDB: Showing metabocard for N-succinyl-(2S,6S)-2,6-diaminoheptanedioic acid (MMDBc0056156)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:18:18 UTC

Update Date

2022-08-12 20:09:36 UTC

Metabolite ID

MMDBc0056156

Metabolite Identification

Common Name

N-succinyl-(2S,6S)-2,6-diaminoheptanedioic acid

Description

N2-Succinyl-L,L-diamino-6-ketopimelate, also known as N-succinyl-(2S,6S)-2,6-diaminoheptanedioate, 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. Based on a literature review very few articles have been published on N2-Succinyl-L,L-diamino-6-ketopimelate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222182D          

 22 21  0  0  1  0            999 V2000
    3.3979    3.8842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5877    4.0401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9379    4.5078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6384    5.4433    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4485    5.2874    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0476    3.4164    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.7481    4.3519    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.0983    4.8196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9886    5.9110    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0181    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3177    2.6369    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.2882    4.9755    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.3683    4.0401    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    8.7987    5.7551    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7186    6.6906    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.6974    2.9487    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9675    4.3519    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8283    3.4164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4780    2.9487    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7776    4.1960    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2080    3.7283    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
  5  4  1  0  0  0  0
  6  2  1  0  0  0  0
  7  3  1  0  0  0  0
  8  4  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  7  1  0  0  0  0
  6 12  1  1  0  0  0
  7 13  1  1  0  0  0
 13  8  2  0  0  0  0
  8 14  1  4  0  0  0
 15  9  2  0  0  0  0
 16  9  1  0  0  0  0
 17 10  2  0  0  0  0
 18 10  1  0  0  0  0
 19 11  2  0  0  0  0
 20 11  1  0  0  0  0
  6 21  1  1  0  0  0
  7 22  1  1  0  0  0
M  CHG  2  14  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0056156

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/p-2/t6-,7-/m0/s1

> <INCHI_KEY>
GLXUWZBUPATPBR-BQBZGAKWSA-L

> <FORMULA>
C11H16N2O7

> <MOLECULAR_WEIGHT>
288.257

> <EXACT_MASS>
288.096848023

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
26.40018975759263

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-{[(1S,5S)-5-amino-1,5-dicarboxypentyl]-C-hydroxycarbonimidoyl}propanoate

> <JCHEM_LOGP>
-2.9472963276592634

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.5901543406295393

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.9057477622658001

> <JCHEM_PKA_STRONGEST_BASIC>
9.526628437941618

> <JCHEM_POLAR_SURFACE_AREA>
176.16999999999996

> <JCHEM_REFRACTIVITY>
85.8856

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
3-{[(1S,5S)-5-amino-1,5-dicarboxypentyl]-C-hydroxycarbonimidoyl}propanoate

> <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       6.343   7.250   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.830   7.541   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.351   8.415   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.392  10.161   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      13.904   9.870   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.822   6.377   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.863   8.124   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      11.383   8.997   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.912  11.034   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.310   6.668   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.367   6.668   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0       4.326   4.922   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       9.871   9.288   0.000  0.00  0.00           N+0
HETATM   14  O   UNK     0      11.888   7.541   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0      16.424  10.743   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      14.408  12.489   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0       1.302   5.504   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.806   8.124   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      10.879   6.377   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       8.359   5.504   0.000  0.00  0.00           O+0
HETATM   21  H   UNK     0       3.318   7.833   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       7.855   6.959   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    7                                                       
CONECT    4    5    8                                                       
CONECT    5    4    9                                                       
CONECT    6    2   10   12   21                                             
CONECT    7    3   11   13   22                                             
CONECT    8    4   13   14                                                  
CONECT    9    5   15   16                                                  
CONECT   10    6   17   18                                                  
CONECT   11    7   19   20                                                  
CONECT   12    6                                                            
CONECT   13    7    8                                                       
CONECT   14    8                                                            
CONECT   15    9                                                            
CONECT   16    9                                                            
CONECT   17   10                                                            
CONECT   18   10                                                            
CONECT   19   11                                                            
CONECT   20   11                                                            
CONECT   21    6                                                            
CONECT   22    7                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   42    0
END

Synonyms

Value	Source
N-(3-Carboxylatopropionyl)-LL-2,6-diaminopimelate dianion	ChEBI
N-Succinyl-(2S,6S)-2,6-diaminoheptanedioate	ChEBI
N-(3-Carboxylatopropionyl)-LL-2,6-diaminopimelic acid dianion	Generator
N-Succinyl-(2S,6S)-2,6-diaminoheptanedioic acid	Generator
N2-Succinyl-L,L-diamino-6-ketopimelic acid	Generator

Molecular Formula

C₁₁H₁₆N₂O₇

Average Mass

288.257

Monoisotopic Mass

288.096848023

IUPAC Name

3-{[(1S,5S)-5-amino-1,5-dicarboxypentyl]-C-hydroxycarbonimidoyl}propanoate

Traditional Name

3-{[(1S,5S)-5-amino-1,5-dicarboxypentyl]-C-hydroxycarbonimidoyl}propanoate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C11H18N2O7/c12-6(10(17)18)2-1-3-7(11(19)20)13-8(14)4-5-9(15)16/h6-7H,1-5,12H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)/p-2/t6-,7-/m0/s1

InChI Key

GLXUWZBUPATPBR-BQBZGAKWSA-L

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
Alpha-amino acid
L-alpha-amino acid
Tricarboxylic acid or derivatives
Fatty amide
N-acyl-amine
Fatty acyl
Carboxamide group
Carboxylic acid salt
Secondary carboxylic acid amide
Amino acid
Carboxylic acid
Organic oxide
Amine
Primary amine
Organooxygen compound
Organonitrogen compound
Organopnictogen compound
Primary aliphatic amine
Organic oxygen compound
Organic nitrogen compound
Organic salt
Carbonyl group
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

N-acyl-L-alpha-amino acid anion (CHEBI:58087 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.9	ChemAxon
pKa (Strongest Acidic)	1.91	ChemAxon
pKa (Strongest Basic)	9.53	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	176.17 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	85.89 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

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

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
Bacteria	Proteobacteria	381	Human ; Human feces; Pig ; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Dog ; Lion ; Chicken ; American dog tick
Bacteria	Actinobacteria	4	Human
Bacteria	Firmicutes	7	Human ; Human feces

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

10123250

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11948934

PDB ID

Not Available

ChEBI ID

58087

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-succinyl-(2S,6S)-2,6-diaminoheptanedioic acid (MMDBc0056156)

MOL for #<Metabolite:0x00007fecec008ee0>

3D MOL for #<Metabolite:0x00007fecec008ee0>

3D SDF for #<Metabolite:0x00007fecec008ee0>

3D-SDF for #<Metabolite:0x00007fecec008ee0>

PDB for #<Metabolite:0x00007fecec008ee0>

3D PDB for #<Metabolite:0x00007fecec008ee0>

SMILES for #<Metabolite:0x00007fecec008ee0>

INCHI for #<Metabolite:0x00007fecec008ee0>

Structure for #<Metabolite:0x00007fecec008ee0>

3D Structure for #<Metabolite:0x00007fecec008ee0>