MiMeDB: Showing metabocard for glutamyl-meso-diaminopimelate (MMDBc0000754)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:54:15 UTC

Update Date

2022-08-31 06:11:57 UTC

Metabolite ID

MMDBc0000754

Metabolite Identification

Common Name

glutamyl-meso-diaminopimelate

Description

gamma-D-glutamyl-meso-diaminopimelic acid, also known as gamma-D-glu-mdap or ie-dap, belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond. gamma-D-glutamyl-meso-diaminopimelic acid is a very strong basic compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304041920162D          

 22 21  0  0  1  0            999 V2000
   12.6177    4.8099    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.6177    3.9849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.9033    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1888    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7599    3.9849    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.0454    3.5724    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3309    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3309    4.8099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.6164    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9020    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1875    3.5724    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.1875    2.7474    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.4730    3.9849    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7586    3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4730    4.8099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7599    4.8099    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0454    5.2224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.4743    5.2224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    3.5724    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0467    3.9849    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.3322    2.7474    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  6  5  1  0  0  0  0
  6  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  0  0  0  0
 12 13  1  1  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  6 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  2  0  0  0  0
  2 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000754

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C12H21N3O7/c13-6(10(17)18)2-1-3-8(12(21)22)15-9(16)5-4-7(14)11(19)20/h6-8H,1-5,13-14H2,(H,15,16)(H,17,18)(H,19,20)(H,21,22)/t6-,7+,8+/m0/s1

> <INCHI_KEY>
QIFGMZZTJRULMA-XLPZGREQSA-N

> <FORMULA>
C12H21N3O7

> <MOLECULAR_WEIGHT>
319.314

> <EXACT_MASS>
319.137950028

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
31.1607312445176

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,6R)-2-amino-6-[(4R)-4-amino-4-carboxybutanamido]heptanedioic acid

> <ALOGPS_LOGP>
-3.96

> <JCHEM_LOGP>
-6.533019159124372

> <ALOGPS_LOGS>
-1.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
2.191827567332613

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5938813442063555

> <JCHEM_PKA_STRONGEST_BASIC>
9.733428831221353

> <JCHEM_POLAR_SURFACE_AREA>
193.03999999999996

> <JCHEM_REFRACTIVITY>
71.7272

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.87e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ie-dap

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-APR-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-APR-19         0                                  
HETATM    1  N   UNK     0      23.553   8.978   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      23.553   7.438   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.219   6.668   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      20.886   7.438   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      19.552   6.668   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      18.218   7.438   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      16.885   6.668   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      15.551   7.438   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      15.551   8.978   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      14.217   6.668   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.884   7.438   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      11.550   6.668   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0      11.550   5.128   0.000  0.00  0.00           N+0
HETATM   14  C   UNK     0      10.216   7.438   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.883   6.668   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      10.216   8.978   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      18.218   8.978   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      16.885   9.748   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      19.552   9.748   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      24.887   6.668   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      26.221   7.438   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      24.887   5.128   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   20                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   17                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    6   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20    2   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   42    0
END

Synonyms

Value	Source
gamma-D-Glu-mdap	ChEBI
IE-dap	ChEBI
g-D-Glu-mdap	Generator
Γ-D-glu-mdap	Generator
g-D-Glutamyl-meso-diaminopimelate	Generator
g-D-Glutamyl-meso-diaminopimelic acid	Generator
gamma-D-Glutamyl-meso-diaminopimelate	Generator
Γ-D-glutamyl-meso-diaminopimelate	Generator
Γ-D-glutamyl-meso-diaminopimelic acid	Generator

Molecular Formula

C₁₂H₂₁N₃O₇

Average Mass

319.314

Monoisotopic Mass

319.137950028

IUPAC Name

(2S,6R)-2-amino-6-[(4R)-4-amino-4-carboxybutanamido]heptanedioic acid

Traditional Name

ie-dap

CAS Registry Number

Not Available

SMILES

N[C@@H](CCC[C@@H](NC(=O)CC[C@@H](N)C(O)=O)C(O)=O)C(O)=O

InChI Identifier

InChI=1S/C12H21N3O7/c13-6(10(17)18)2-1-3-8(12(21)22)15-9(16)5-4-7(14)11(19)20/h6-8H,1-5,13-14H2,(H,15,16)(H,17,18)(H,19,20)(H,21,22)/t6-,7+,8+/m0/s1

InChI Key

QIFGMZZTJRULMA-XLPZGREQSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as dipeptides. These are organic compounds containing a sequence of exactly two alpha-amino acids joined by a peptide bond.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Dipeptides

Alternative Parents

Substituents

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

tricarboxylic acid (CHEBI:59271 )
D-alpha-amino acid (CHEBI:59271 )
D-glutamic acid derivative (CHEBI:59271 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.87 g/L	ALOGPS
logP	-4	ALOGPS
logP	-6.5	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	1.59	ChemAxon
pKa (Strongest Basic)	9.73	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	193.04 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	71.73 m³·mol⁻¹	ChemAxon
Polarizability	31.16 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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_3_22) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available	2022-08-09	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available	2022-08-09	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-22	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

Not Available

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	Actinobacteria	1	Human ; Human feces	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	1	Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen

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

HMDB0240360

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

45480617

PDB ID

Not Available

ChEBI ID

59271

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Showing metabocard for glutamyl-meso-diaminopimelate (MMDBc0000754)

MOL for #<Metabolite:0x00007fd0f800f3b8>

3D MOL for #<Metabolite:0x00007fd0f800f3b8>

3D SDF for #<Metabolite:0x00007fd0f800f3b8>

3D-SDF for #<Metabolite:0x00007fd0f800f3b8>

PDB for #<Metabolite:0x00007fd0f800f3b8>

3D PDB for #<Metabolite:0x00007fd0f800f3b8>

SMILES for #<Metabolite:0x00007fd0f800f3b8>

INCHI for #<Metabolite:0x00007fd0f800f3b8>

Structure for #<Metabolite:0x00007fd0f800f3b8>

3D Structure for #<Metabolite:0x00007fd0f800f3b8>