MiMeDB: Showing metabocard for L-Ala-gamma-D-Glu-Dap (MMDBc0030199)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:58:04 UTC

Update Date

2022-08-31 17:40:37 UTC

Metabolite ID

MMDBc0030199

Metabolite Identification

Common Name

L-Ala-gamma-D-Glu-Dap

Description

L-ala-gamma-D-glu-DAP is a member of the chemical class known as Hybrid Peptides. These are compounds containing at least two different types of amino acids (alpha, beta, gamma, delta). L-alanyl-gamma-D-glutamyl-meso-diaminopimelate is related to MppA. MppA is a periplasmic binding protein in Escherichia coli essential for uptake of the cell wall murein tripeptide L-alanyl-gamma-D-glutamyl-meso-diaminopimelate. (PMID 10438753 )

Structure

MOL SDF PDB SMILES InChI

Structure #1
  Mrv0541 02241207332D          

 22 22  0  0  0  0            999 V2000
    6.4302    6.1875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5737    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    3.7125    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
    3.5724    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    6.1875    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.8592    1.2375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    4.5375    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.1447    2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    3.7125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  3  9  1  0  0  0  0
  4 10  2  0  0  0  0
  5  6  1  0  0  0  0
  5  8  1  0  0  0  0
  6 11  1  0  0  0  0
  7 12  1  0  0  0  0
  7 14  1  0  0  0  0
  8 13  1  0  0  0  0
 16  8  1  4  0  0  0
  9 15  2  0  0  0  0
  9 17  1  0  0  0  0
 10 17  1  0  0  0  0
 18 10  1  4  0  0  0
 11 19  2  0  0  0  0
 11 20  1  0  0  0  0
 12 16  2  0  0  0  0
 12 21  1  0  0  0  0
 13 18  2  0  0  0  0
 13 22  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030199

> <DATABASE_NAME>
MIME

> <SMILES>
CC(N)C(O)=NC(CCC(O)=O)C(O)=NC1=CC=CC(=N)N1

> <INCHI_IDENTIFIER>
InChI=1S/C13H19N5O4/c1-7(14)12(21)16-8(5-6-11(19)20)13(22)18-10-4-2-3-9(15)17-10/h2-4,7-8H,5-6,14H2,1H3,(H,16,21)(H,19,20)(H3,15,17,18,22)

> <INCHI_KEY>
IBYVCSBRMYGDRR-UHFFFAOYSA-N

> <FORMULA>
C13H19N5O4

> <MOLECULAR_WEIGHT>
309.3211

> <EXACT_MASS>
309.143704121

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
31.28721207536737

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
4-[(2-amino-1-hydroxypropylidene)amino]-4-[(6-imino-1,6-dihydropyridin-2-yl)-C-hydroxycarbonimidoyl]butanoic acid

> <ALOGPS_LOGP>
-2.29

> <JCHEM_LOGP>
-4.27086585119958

> <ALOGPS_LOGS>
-3.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
4.286055888640839

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.17206521731895563

> <JCHEM_PKA_STRONGEST_BASIC>
18.930019258614216

> <JCHEM_POLAR_SURFACE_AREA>
164.38

> <JCHEM_REFRACTIVITY>
99.8819

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.34e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-[(2-amino-1-hydroxypropylidene)amino]-4-[(6-imino-1H-pyridin-2-yl)-C-hydroxycarbonimidoyl]butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      12.003  11.550   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      16.004   6.160   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.004   4.620   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      14.671   6.930   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      10.669  10.780   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.671   3.850   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      13.337   6.160   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.669   9.240   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      10.669   6.160   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0       9.336  11.550   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0      14.671   2.310   0.000  0.00  0.00           N+0
HETATM   16  N   UNK     0       9.336   8.470   0.000  0.00  0.00           N+0
HETATM   17  N   UNK     0      13.337   4.620   0.000  0.00  0.00           N+0
HETATM   18  N   UNK     0      12.003   6.930   0.000  0.00  0.00           N+0
HETATM   19  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       4.001   6.930   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      12.003   8.470   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      10.669   4.620   0.000  0.00  0.00           O+0
CONECT    1    7                                                            
CONECT    2    3    4                                                       
CONECT    3    2    9                                                       
CONECT    4    2   10                                                       
CONECT    5    6    8                                                       
CONECT    6    5   11                                                       
CONECT    7    1   12   14                                                  
CONECT    8    5   13   16                                                  
CONECT    9    3   15   17                                                  
CONECT   10    4   17   18                                                  
CONECT   11    6   19   20                                                  
CONECT   12    7   16   21                                                  
CONECT   13    8   18   22                                                  
CONECT   14    7                                                            
CONECT   15    9                                                            
CONECT   16    8   12                                                       
CONECT   17    9   10                                                       
CONECT   18   10   13                                                       
CONECT   19   11                                                            
CONECT   20   11                                                            
CONECT   21   12                                                            
CONECT   22   13                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

Synonyms

Value	Source
L-Ala-g-D-glu-dap	Generator
L-Ala-γ-D-glu-dap	Generator
4-[(2-Amino-1-hydroxypropylidene)amino]-4-[(6-imino-1,6-dihydropyridin-2-yl)-C-hydroxycarbonimidoyl]butanoate	Generator

Molecular Formula

C₁₃H₁₉N₅O₄

Average Mass

309.3211

Monoisotopic Mass

309.143704121

IUPAC Name

4-[(2-amino-1-hydroxypropylidene)amino]-4-[(6-imino-1,6-dihydropyridin-2-yl)-C-hydroxycarbonimidoyl]butanoic acid

Traditional Name

4-[(2-amino-1-hydroxypropylidene)amino]-4-[(6-imino-1H-pyridin-2-yl)-C-hydroxycarbonimidoyl]butanoic acid

CAS Registry Number

Not Available

SMILES

CC(N)C(O)=NC(CCC(O)=O)C(O)=NC1=CC=CC(=N)N1

InChI Identifier

InChI=1S/C13H19N5O4/c1-7(14)12(21)16-8(5-6-11(19)20)13(22)18-10-4-2-3-9(15)17-10/h2-4,7-8H,5-6,14H2,1H3,(H,16,21)(H,19,20)(H3,15,17,18,22)

InChI Key

IBYVCSBRMYGDRR-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acylaminosugars. These are organic compounds containing a sugar linked to a chain through N-acyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Acylaminosugars

Alternative Parents

Substituents

Oligosaccharide phosphate
Oligosaccharide
Hexacarboxylic acid or derivatives
Acylaminosugar
Saccharolipid
Hexose phosphate
N-acyl-alpha-hexosamine
C-glucuronide
C-glycosyl compound
Glycosyl compound
O-glycosyl compound
Beta-hydroxy acid
Ketal
Fatty acid ester
Dialkyl phosphate
Fatty amide
Fatty acyl
Hydroxy acid
N-acyl-amine
Alkyl phosphate
Pyran
Organic phosphoric acid derivative
Oxane
Phosphoric acid ester
Amino acid or derivatives
Secondary alcohol
Secondary carboxylic acid amide
Amino acid
Carboxamide group
Carboxylic acid ester
1,2-aminoalcohol
Organoheterocyclic compound
Carboxylic acid derivative
Acetal
Carboxylic acid
Oxacycle
Primary amine
Carbonyl group
Organic nitrogen compound
Primary aliphatic amine
Alcohol
Amine
Primary alcohol
Organic oxide
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.13 g/L	ALOGPS
logP	-2.3	ALOGPS
logP	-4.3	ChemAxon
logS	-3.4	ALOGPS
pKa (Strongest Acidic)	-0.17	ChemAxon
pKa (Strongest Basic)	18.93	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	164.38 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	99.88 m³·mol⁻¹	ChemAxon
Polarizability	31.29 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	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	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

656477

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Li H, Park JT: The periplasmic murein peptide-binding protein MppA is a negative regulator of multiple antibiotic resistance in Escherichia coli. J Bacteriol. 1999 Aug;181(16):4842-7. doi: 10.1128/JB.181.16.4842-4847.1999. [PubMed:10438753 ]
van der Werf MJ, Overkamp KM, Muilwijk B, Coulier L, Hankemeier T: Microbial metabolomics: toward a platform with full metabolome coverage. Anal Biochem. 2007 Nov 1;370(1):17-25. doi: 10.1016/j.ab.2007.07.022. Epub 2007 Aug 1. [PubMed:17765195 ]
Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, Muniz-Rascado L, Bonavides-Martinez C, Paley S, Krummenacker M, Altman T, Kaipa P, Spaulding A, Pacheco J, Latendresse M, Fulcher C, Sarker M, Shearer AG, Mackie A, Paulsen I, Gunsalus RP, Karp PD: EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90. doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21. [PubMed:21097882 ]

Showing metabocard for L-Ala-gamma-D-Glu-Dap (MMDBc0030199)

MOL for #<Metabolite:0x00007f9238499068>

3D MOL for #<Metabolite:0x00007f9238499068>

3D SDF for #<Metabolite:0x00007f9238499068>

3D-SDF for #<Metabolite:0x00007f9238499068>

PDB for #<Metabolite:0x00007f9238499068>

3D PDB for #<Metabolite:0x00007f9238499068>

SMILES for #<Metabolite:0x00007f9238499068>

INCHI for #<Metabolite:0x00007f9238499068>

Structure for #<Metabolite:0x00007f9238499068>

3D Structure for #<Metabolite:0x00007f9238499068>