D-Methionine (YMDB00816)

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Identification

YMDB ID

YMDB00816

Name

D-Methionine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

D-Methionine, also known as MED, belongs to the class of organic compounds known as methionine and derivatives. Methionine and derivatives are compounds containing methionine or a derivative thereof resulting from reaction of methionine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom. D-Methionine is a very strong basic compound (based on its pKa). D-Methionine exists in both E. coli (prokaryote) and yeast (eukaryote).

Structure

MOL SDF PDB SMILES InChI

Synonyms

(2R)-2-amino-4-(methylsulfanyl)butanoic acid
(R)-2-amino-4-(methylthio)butanoic acid
(R)-methionine
d-2-Amino-4-(methylthio)butyric acid
D-Methionin
D-Methionine
D-Metionien
Methionine
Methionine d-form
Methionine, D-
R-Methionine
MED
(2R)-2-Amino-4-(methylsulfanyl)butanoate
(2R)-2-Amino-4-(methylsulphanyl)butanoate
(2R)-2-Amino-4-(methylsulphanyl)butanoic acid
(R)-2-Amino-4-(methylthio)butanoate
D-2-Amino-4-(methylthio)butyrate
L-Isomer methionine
L-Methionine
Pedameth
Liquimeth
Methionine, L isomer
Methionine, L-isomer

CAS number

348-67-4

Weight

Average: 149.211
Monoisotopic: 149.051049291

InChI Key

FFEARJCKVFRZRR-SCSAIBSYSA-N

InChI

InChI=1S/C5H11NO2S/c1-9-3-2-4(6)5(7)8/h4H,2-3,6H2,1H3,(H,7,8)/t4-/m1/s1

IUPAC Name

(2R)-2-amino-4-(methylsulfanyl)butanoic acid

Traditional IUPAC Name

D-methionine

Chemical Formula

C₅H₁₁NO₂S

SMILES

CSCC[C@@H](N)C(O)=O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as methionine and derivatives. Methionine and derivatives are compounds containing methionine or a derivative thereof resulting from reaction of methionine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

Methionine and derivatives

Alternative Parents

Substituents

Methionine or derivatives
Alpha-amino acid
D-alpha-amino acid
Thia fatty acid
Fatty acid
Fatty acyl
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Thioether
Sulfenyl compound
Dialkylthioether
Amine
Organic oxygen compound
Primary amine
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Organic nitrogen compound
Primary aliphatic amine
Carbonyl group
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

D-alpha-amino acid (CHEBI:16867 )
methionine (CHEBI:16867 )
Other amino acids (C00855 )

Physical Properties

State

Solid

Charge

Melting point

213 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	23.9 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.2	ChemAxon
logS	-0.8	ALOGPS
pKa (Strongest Acidic)	2.53	ChemAxon
pKa (Strongest Basic)	9.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	37.59 m³·mol⁻¹	ChemAxon
Polarizability	15.46 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Not Available

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0mbd-9200000000-77e5cfb78936ad02d71c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-67e023372cdbac09cb36	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-9800000000-1e589df1b14865d84d74	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-056r-9000000000-efb0cddabddaf5231dbd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-6900000000-9ef89c92bce71adb0b81	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-9300000000-8507980760c8afb7f454	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-9000000000-544c2c943904dcca737e	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

References

References:

Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Yow, G. Y., Uo, T., Yoshimura, T., Esaki, N. (2004). "D-amino acid N-acetyltransferase of Saccharomyces cerevisiae: a close homologue of histone acetyltransferase Hpa2p acting exclusively on free D-amino acids." Arch Microbiol 182:396-403.15375647

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	16867
HMDB ID	Not Available
Pubchem Compound ID	84815
Kegg ID	C00855
ChemSpider ID	76512
FOODB ID	Not Available
Wikipedia	Methionine
BioCyc ID	MET

Enzymes

Protein Details

1. N-acetyltransferase HPA3

General function:: Involved in N-acetyltransferase activity
Specific function:: N-acetyltransferase whose physiological acetyl acceptor substrate is still unknown. In vitro, histone acetylation is very weak
Gene Name:: HPA3
Uniprot ID:: P39979
Molecular weight:: 20698.5

Reactions

acetyl-CoA + a D-amino acid → CoA + an N-acetyl-D-amino acid

Structure for #<Compound:0xa8479e30>

Enzymes

Reactions