MiMeDB: Showing metabocard for Glycyl-L-methionine (MMDBc0049920)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:46:19 UTC

Update Date

2024-04-30 20:40:35 UTC

Metabolite ID

MMDBc0049920

Metabolite Identification

Common Name

Glycyl-L-methionine

Description

Glycyl-Methionine is a dipeptide composed of glycine and methionine. It is an incomplete breakdown product of protein digestion or protein catabolism. Some dipeptides are known to have physiological or cell-signaling effects although most are simply short-lived intermediates on their way to specific amino acid degradation pathways following further proteolysis. This dipeptide has not yet been identified in human tissues or biofluids and so it is classified as an 'Expected' metabolite.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652304062013422D          

 13 12  0  0  0  0            999 V2000
    2.9980    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7125    2.1434    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    4.4270    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    2.1434    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    2.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2849    3.3809    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9993    2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7138    2.5559    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8559    3.3809    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5704    3.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1414    3.7934    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
  5 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049920

> <DATABASE_NAME>
MIME

> <SMILES>
CSCCC(NC(=O)CN)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C7H14N2O3S/c1-13-3-2-5(7(11)12)9-6(10)4-8/h5H,2-4,8H2,1H3,(H,9,10)(H,11,12)

> <INCHI_KEY>
PFMUCCYYAAFKTH-UHFFFAOYSA-N

> <FORMULA>
C7H14N2O3S

> <MOLECULAR_WEIGHT>
206.263

> <EXACT_MASS>
206.072513014

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
20.921064839707658

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-(2-aminoacetamido)-4-(methylsulfanyl)butanoic acid

> <ALOGPS_LOGP>
-1.99

> <JCHEM_LOGP>
-3.2969630948228046

> <ALOGPS_LOGS>
-1.23

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.761709498601686

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.7295472502281304

> <JCHEM_PKA_STRONGEST_BASIC>
8.139567138504848

> <JCHEM_POLAR_SURFACE_AREA>
92.42000000000002

> <JCHEM_REFRACTIVITY>
50.389500000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.23e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-(2-aminoacetamido)-4-(methylsulfanyl)butanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-20         0                                  
HETATM    1  C   UNK     0       5.596   4.771   0.000  0.00  0.00           C+0
HETATM    2  S   UNK     0       6.930   4.001   0.000  0.00  0.00           S+0
HETATM    3  C   UNK     0       8.264   4.771   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.597   4.001   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.931   4.771   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      12.265   4.001   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      13.598   4.771   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      13.598   6.311   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      14.932   4.001   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      16.266   4.771   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      10.931   6.311   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      12.265   7.081   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.597   7.081   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   11                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9                                                            
CONECT   11    5   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   24    0
END

COMPND    HMDB0028847
HETATM    1  C1  UNL     1      -4.103  -1.259  -0.230  1.00  0.00           C  
HETATM    2  S1  UNL     1      -3.555  -0.223   1.159  1.00  0.00           S  
HETATM    3  C2  UNL     1      -2.231   0.931   0.622  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.055   0.087   0.279  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.161   0.841  -0.185  1.00  0.00           C  
HETATM    6  N1  UNL     1       1.170  -0.199  -0.455  1.00  0.00           N  
HETATM    7  C5  UNL     1       2.433  -0.188   0.157  1.00  0.00           C  
HETATM    8  O1  UNL     1       2.724   0.727   0.958  1.00  0.00           O  
HETATM    9  C6  UNL     1       3.418  -1.238  -0.131  1.00  0.00           C  
HETATM   10  N2  UNL     1       4.633  -1.007   0.619  1.00  0.00           N  
HETATM   11  C7  UNL     1      -0.087   1.614  -1.443  1.00  0.00           C  
HETATM   12  O2  UNL     1       0.488   1.360  -2.531  1.00  0.00           O  
HETATM   13  O3  UNL     1      -0.992   2.663  -1.418  1.00  0.00           O  
HETATM   14  H1  UNL     1      -3.940  -0.770  -1.203  1.00  0.00           H  
HETATM   15  H2  UNL     1      -3.620  -2.247  -0.240  1.00  0.00           H  
HETATM   16  H3  UNL     1      -5.197  -1.408  -0.098  1.00  0.00           H  
HETATM   17  H4  UNL     1      -2.598   1.422  -0.315  1.00  0.00           H  
HETATM   18  H5  UNL     1      -2.066   1.621   1.448  1.00  0.00           H  
HETATM   19  H6  UNL     1      -0.732  -0.523   1.150  1.00  0.00           H  
HETATM   20  H7  UNL     1      -1.306  -0.646  -0.526  1.00  0.00           H  
HETATM   21  H8  UNL     1       0.546   1.568   0.551  1.00  0.00           H  
HETATM   22  H9  UNL     1       0.935  -0.963  -1.120  1.00  0.00           H  
HETATM   23  H10 UNL     1       3.050  -2.260   0.147  1.00  0.00           H  
HETATM   24  H11 UNL     1       3.633  -1.324  -1.232  1.00  0.00           H  
HETATM   25  H12 UNL     1       4.559  -0.075   1.076  1.00  0.00           H  
HETATM   26  H13 UNL     1       4.792  -1.797   1.262  1.00  0.00           H  
HETATM   27  H14 UNL     1      -1.058   3.292  -0.625  1.00  0.00           H  
CONECT    1    2   14   15   16
CONECT    2    3
CONECT    3    4   17   18
CONECT    4    5   19   20
CONECT    5    6   11   21
CONECT    6    7   22
CONECT    7    8    8    9
CONECT    9   10   23   24
CONECT   10   25   26
CONECT   11   12   12   13
CONECT   13   27
END

Synonyms

Value	Source
g-m Dipeptide	HMDB
Gly-met	HMDB
Glycine methionine dipeptide	HMDB
Glycine-methionine dipeptide	HMDB
Glycylmethionine	HMDB
GM Dipeptide	HMDB
L-Glycyl-L-methionine	HMDB
2-[(2-Amino-1-hydroxyethylidene)amino]-4-(methylsulfanyl)butanoate	HMDB
2-[(2-Amino-1-hydroxyethylidene)amino]-4-(methylsulphanyl)butanoate	HMDB
2-[(2-Amino-1-hydroxyethylidene)amino]-4-(methylsulphanyl)butanoic acid	HMDB

Molecular Formula

C₇H₁₄N₂O₃S

Average Mass

206.263

Monoisotopic Mass

206.072513014

IUPAC Name

2-(2-aminoacetamido)-4-(methylsulfanyl)butanoic acid

Traditional Name

2-(2-aminoacetamido)-4-(methylsulfanyl)butanoic acid

CAS Registry Number

Not Available

SMILES

CSCCC(NC(=O)CN)C(O)=O

InChI Identifier

InChI=1S/C7H14N2O3S/c1-13-3-2-5(7(11)12)9-6(10)4-8/h5H,2-4,8H2,1H3,(H,9,10)(H,11,12)

InChI Key

PFMUCCYYAAFKTH-UHFFFAOYSA-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
Methionine or derivatives
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid amide
Alpha-amino acid or derivatives
Thia fatty acid
Fatty acyl
Fatty acid
Amino acid or derivatives
Carboxamide group
Amino acid
Secondary carboxylic acid amide
Carboxylic acid
Monocarboxylic acid or derivatives
Dialkylthioether
Sulfenyl compound
Thioether
Organonitrogen compound
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Primary aliphatic amine
Organic oxide
Carbonyl group
Organooxygen compound
Organosulfur compound
Primary amine
Amine
Organopnictogen compound
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
Water Solubility	12.3 g/L	ALOGPS
logP	-2	ALOGPS
logP	-3.3	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	3.73	ChemAxon
pKa (Strongest Basic)	8.14	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	92.42 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	50.39 m³·mol⁻¹	ChemAxon
Polarizability	20.92 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

Feces

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	Firmicutes	362	Human feces; Human pleural fluid plaque; Pig ; Human ; Human supragingival plaque; Human saliva; Cattle ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	171	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria	Actinobacteria	15	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	114	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	129	Human feces; Human appendix biopsy; Human ; Human stool; Human urine; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Bacteria	Proteobacteria	7	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria	Firmicutes	27	Human feces; Human pleural fluid plaque; Pig ; Human ; Human supragingival plaque; Human saliva; Cattle ; Human stool; Human subgingival plaque	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria/Eubacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB
Human Feces	Detected but not Quantified						Adult (>18 years old)	Both	Normal	HMDB	25037050

External Links

HMDB ID

HMDB0028847

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB111882

KNApSAcK ID

Not Available

Chemspider ID

87361

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

96757

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Cascieri T, Mallette MF: Peptide utilization by Pseudomonas putida and Pseudomonas maltophilia. J Gen Microbiol. 1976 Feb;92(2):283-95. doi: 10.1099/00221287-92-2-283. [PubMed:1255131 ]
Cascieri T, Mallette MF: Intracellular peptide hydrolysis by Pseudomonas putida and Pseudomonas maltophilia. J Gen Microbiol. 1976 Feb;92(2):296-303. doi: 10.1099/00221287-92-2-296. [PubMed:1255132 ]
Cascieri T Jr, Mallette MF: New method for study of peptide transport in bacteria. Appl Microbiol. 1974 Mar;27(3):457-63. doi: 10.1128/am.27.3.457-463.1974. [PubMed:4596381 ]
Pan Y, Bender PK, Akers RM, Webb KE Jr: Methionine-containing peptides can be used as methionine sources for protein accretion in cultured C2C12 and MAC-T cells. J Nutr. 1996 Jan;126(1):232-41. doi: 10.1093/jn/126.1.232. [PubMed:8558306 ]
Nagy Z, Fabian I, Sovago I: Thermodynamic, kinetic and structural studies on the ternary palladium(II) complexes of thioether ligands. J Inorg Biochem. 2000 Apr;79(1-4):129-38. doi: 10.1016/s0162-0134(99)00157-9. [PubMed:10830857 ]
Boka B, Nagy Z, Varnagy K, Sovago I: Solution equilibria and structural characterisation of the palladium(II) and mixed metal complexes of peptides containing methionyl residues. J Inorg Biochem. 2001 Jan 15;83(2-3):77-89. doi: 10.1016/s0162-0134(00)00196-3. [PubMed:11237266 ]
Nagy Z, Fabian I, Sovago I: [Model studies on the transport processes of anticancer platinum complexes]. Acta Pharm Hung. 2000 Jul-Dec;70(3-6):211-22. [PubMed:11379028 ]
Williams WA, Zhang RG, Zhou M, Joachimiak G, Gornicki P, Missiakas D, Joachimiak A: The membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus binds the dipeptide GlyMet via side chain interactions. Biochemistry. 2004 Dec 28;43(51):16193-202. doi: 10.1021/bi048877o. [PubMed:15610013 ]
Bugarcic ZD, Rosic J, Petrovic B, Summa N, Puchta R, van Eldik R: Kinetics and mechanism of the substitution reactions of [PtCl(bpma)]+, [PtCl(gly-met-S,N,N)] and their aqua analogues with L-methionine, glutathione and 5'-GMP. J Biol Inorg Chem. 2007 Nov;12(8):1141-50. doi: 10.1007/s00775-007-0283-1. Epub 2007 Aug 21. [PubMed:17710451 ]
Morozova OB, Korchak SE, Vieth HM, Yurkovskaya AV: Photo-CIDNP study of transient radicals of Met-Gly and Gly-Met peptides in aqueous solution at variable pH. J Phys Chem B. 2009 May 21;113(20):7398-406. doi: 10.1021/jp8112182. [PubMed:19438284 ]
Yang X, Wu Z, Wang X, Yang C, Xu H, Shen Y: Crystal structure of lipoprotein GNA1946 from Neisseria meningitidis. J Struct Biol. 2009 Dec;168(3):437-43. doi: 10.1016/j.jsb.2009.09.001. Epub 2009 Sep 3. [PubMed:19733245 ]

Showing metabocard for Glycyl-L-methionine (MMDBc0049920)

MOL for #<Metabolite:0x00007f921a755c70>

3D MOL for #<Metabolite:0x00007f921a755c70>

3D SDF for #<Metabolite:0x00007f921a755c70>

3D-SDF for #<Metabolite:0x00007f921a755c70>

PDB for #<Metabolite:0x00007f921a755c70>

3D PDB for #<Metabolite:0x00007f921a755c70>

SMILES for #<Metabolite:0x00007f921a755c70>

INCHI for #<Metabolite:0x00007f921a755c70>

Structure for #<Metabolite:0x00007f921a755c70>

3D Structure for #<Metabolite:0x00007f921a755c70>