MiMeDB: Showing metabocard for D-methionine (MMDBc0000286)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-10-28 00:02:24 UTC

Update Date

2022-08-31 00:16:52 UTC

Metabolite ID

MMDBc0000286

Metabolite Identification

Common Name

D-methionine

Description

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2R)-2-Amino-4-(methylsulfanyl)butanoic acid	ChEBI
(R)-2-Amino-4-(methylthio)butanoic acid	ChEBI
(R)-Methionine	ChEBI
D-2-Amino-4-(methylthio)butyric acid	ChEBI
D-Methionin	ChEBI
MED	ChEBI
(2R)-2-Amino-4-(methylsulfanyl)butanoate	Generator
(2R)-2-Amino-4-(methylsulphanyl)butanoate	Generator
(2R)-2-Amino-4-(methylsulphanyl)butanoic acid	Generator
(R)-2-Amino-4-(methylthio)butanoate	Generator
D-2-Amino-4-(methylthio)butyrate	Generator
L-Isomer methionine	MeSH
L-Methionine	MeSH
Pedameth	MeSH
Liquimeth	MeSH
Methionine, L isomer	MeSH
Methionine, L-isomer	MeSH
Methionine	MeSH

Molecular Formula

C₅H₁₁NO₂S

Average Mass

149.211

Monoisotopic Mass

149.051049291

IUPAC Name

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

Traditional Name

D-methionine

CAS Registry Number

348-67-4

SMILES

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

InChI Identifier

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

InChI Key

FFEARJCKVFRZRR-SCSAIBSYSA-N

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

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	Yes	ChemAxon
Rule of Five	Yes	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 (Non-derivatized) - 70eV, Positive	splash10-0mbd-9200000000-77e5cfb78936ad02d71c	2016-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-2900000000-67e023372cdbac09cb36	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-9800000000-1e589df1b14865d84d74	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-056r-9000000000-efb0cddabddaf5231dbd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-6900000000-9ef89c92bce71adb0b81	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-9300000000-8507980760c8afb7f454	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0002-9000000000-544c2c943904dcca737e	2015-09-15	View Spectrum
1D NMR	¹H NMR Spectrum (1D, D₂O, experimental)		2016-10-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, D₂O, experimental)		2016-10-22	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0007488	Adenosine triphosphate	ADP	Not Available	D-methionine transport via ABC system	VMH	30371894
MMDBr0014935	Adenosine triphosphate	ADP	Methionine import ATP-binding protein MetN	Transport	RHEA	34755880
MMDBr0017848	L-Methionine	D-methionine	Broad substrate specificity amino-acid racemase	Racemization	RHEA	34755880
MMDBr0026120	Acetyl-CoA	Hydrogen Ion	D-amino-acid N-acetyltransferase HPA3	Acetylation	RHEA	34755880
MMDBr0026133	L-Methionine	D-methionine	Broad substrate specificity amino-acid racemase	Racemization	RHEA	34755880
MMDBr0039025	Acetyl-CoA	CoA	D-amino-acid N-acetyltransferase HPA3	Acetylation	RHEA	34755880

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	Firmicutes	397	Human feces; Human pleural fluid plaque; Pig ; Human ; Human supragingival plaque; Human saliva; Cattle ; Human subgingival plaque	Metabolic reconstruction
Bacteria	Proteobacteria	265	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; Turkey ; Lion ; Chicken ; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	128	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	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	1	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	2	Human feces; Human saliva	Metabolic reconstruction; Unknown
Bacteria	Chlamydiae	5	Human ; Sheep ; Cat
Archaea/Archaea	Euryarchaeota	2
Bacteria/NULL	Proteobacteria	1	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; Turkey ; Lion ; Chicken ; Cattle	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

DB02893

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C00855

BioCyc ID

CPD-218

BiGG ID

Not Available

Wikipedia Link

Methionine

METLIN ID

Not Available

PubChem Compound

84815

PDB ID

Not Available

ChEBI ID

16867

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 D-methionine (MMDBc0000286)

MOL for #<Metabolite:0x000055c7989a02d0>

3D MOL for #<Metabolite:0x000055c7989a02d0>

3D SDF for #<Metabolite:0x000055c7989a02d0>

3D-SDF for #<Metabolite:0x000055c7989a02d0>

PDB for #<Metabolite:0x000055c7989a02d0>

3D PDB for #<Metabolite:0x000055c7989a02d0>

SMILES for #<Metabolite:0x000055c7989a02d0>

INCHI for #<Metabolite:0x000055c7989a02d0>

Structure for #<Metabolite:0x000055c7989a02d0>

3D Structure for #<Metabolite:0x000055c7989a02d0>