MiMeDB: Showing metabocard for N-Formyl-L-methionine (MMDBc0000560)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:40:32 UTC

Update Date

2024-04-30 19:33:00 UTC

Metabolite ID

MMDBc0000560

Metabolite Identification

Common Name

N-Formyl-L-methionine

Description

N-formyl-L-methionine is a L-methionine derivative in which one of the hydrogens attached to the nitrogen is replaced by a formyl group. It has a role as a metabolite. It is a proteinogenic amino acid, a N-formyl amino acid and a L-methionine derivative. It is a conjugate acid of a N-formyl-L-methioninate. N-Formyl-L-methionine 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. N-Formyl-L-methionine is effective in the initiation of protein synthesis. The initiating methionine residue enters the ribosome as N-formylmethionyl-tRNA. This process occurs in Escherichia coli and other bacteria as well as in the mitochondria of eukaryotic cells.

Structure

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

Synonyms

Value	Source
(2S)-2-(Formylamino)-4-(methylthio)butanoic acid	ChEBI
Formyl-methionine	ChEBI
N-Formylmethionine	ChEBI
(2S)-2-(Formylamino)-4-(methylthio)butanoate	Generator
Formylmethionine, N	HMDB
N Formylmethionine	HMDB
N-Formyl-L-methionine	KEGG

Molecular Formula

C₆H₁₁NO₃S

Average Mass

177.221

Monoisotopic Mass

177.045963913

IUPAC Name

(2S)-2-formamido-4-(methylsulfanyl)butanoic acid

Traditional Name

N-formylmethionine

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C6H11NO3S/c1-11-3-2-5(6(9)10)7-4-8/h4-5H,2-3H2,1H3,(H,7,8)(H,9,10)/t5-/m0/s1

InChI Key

PYUSHNKNPOHWEZ-YFKPBYRVSA-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
N-acyl-l-alpha-amino acid
N-formyl-alpha-amino acid
N-formyl-alpha amino acid or derivatives
Thia fatty acid
Fatty acid
Fatty acyl
Carboxamide group
Secondary carboxylic acid amide
Dialkylthioether
Sulfenyl compound
Thioether
Monocarboxylic acid or derivatives
Carboxylic acid
Hydrocarbon derivative
Organic oxide
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organopnictogen compound
Organic oxygen compound
Organic nitrogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

proteinogenic amino acid (CHEBI:16552 )
L-methionine derivative (CHEBI:16552 )
N-formyl amino acid (CHEBI:16552 )
Other amino acids (C03145 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	9.75 g/L	ALOGPS
logP	-0.61	ALOGPS
logP	-0.16	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	3.93	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.4 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	42.54 m³·mol⁻¹	ChemAxon
Polarizability	17.59 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
GC-MS	GC-MS Spectrum - GC-MS (2 TMS)	splash10-0pdi-1920000000-7ead52d367d0c14c2f83	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - GC-MS (1 TMS)	splash10-002r-9800000000-d6bd1c4a45710fcff139	2014-06-16	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-004i-1900000000-dbd5e7526844833f2769	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - EI-B (Non-derivatized)	splash10-002b-1931000000-f6d54f9e00989580bf16	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0zi1-0920000000-eff4a723ccd21264f857	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-002r-6900000000-f44202a7297064bce497	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pdj-0920000000-4d46bd9a6a5f645fdee9	2017-09-12	View Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-00di-9410000000-0d6268555c7a6ebf60ef	2017-09-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000y-9200000000-10205de54a16e96cf3ad	2017-08-28	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0900000000-a5b03aa018c68be71432	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-002b-9600000000-e2a1a85ea82026c67c40	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9000000000-4f909deb0784221401df	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9000000000-e07240ba0c7d6b253cf3	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-0002-9000000000-04ba3fa1d5a4d4da730a	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004i-4900000000-b9244ecfa5c3afeec4c8	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03fr-0900000000-6cef5cfd02af4e4f5603	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0fc0-2900000000-ca29f2380d125436464f	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0gx0-9600000000-d8211d4ecddfb71549d2	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0bu0-9200000000-95443fc05ab3a30f1736	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03di-9100000000-61580bdacfbf4ccd3b72	2017-09-14	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 10V, Negative	splash10-002b-9300000000-6b6656d410859495b7d6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-0002-9000000000-36639998e841668381bf	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Negative	splash10-0002-9000000000-00ec72b1c1c573b951a4	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 30V, Negative	splash10-0002-9000000000-42e1592f1bbdcb4b4283	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Negative	splash10-0002-9000000000-c901d1fde297485a1211	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-03e9-9200000000-66fcb11cb1ad675d36b6	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-03di-9000000000-becdef0ad11ee4b6c1a0	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-08gi-9000000000-0cb78961b18f92893c52	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0032-0900000000-8f385306243b675f9f3a	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0faj-4900000000-e575d78a4fb6796b499f	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0ug0-9600000000-fb463674953dd37d24d3	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004j-9800000000-c1e3c8cc0a2b6fb080c7	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0002-9300000000-0ba777d8c80b1cda51d6	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0005-9000000000-7b1e231a15535ddad645	2017-07-26	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-29	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood
Feces
Intestine
Placenta
Urine

Tissue Locations

Intestine
Placenta

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
MMDBr0024779	Water	formate	Peptide deformylase 1	Removal of the N-terminal formyl group	RHEA	34755880
MMDBr0024780	formate	Water	Peptide deformylase	Removal of the N-terminal formyl group	RHEA	34755880
MMDBr0036107	N-Formyl-L-methionine	L-Methionine	Acylamidase	Hydrolysis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference
Prostate cancer		Association	Human Urine	HMDB	19212411

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Verrucomicrobia	1	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	10	Human feces; Human stool; Human ; Human urine; Human sputum; Human saliva; Human subgingival plaque; Human vaginal fluid; Human supragingival plaque	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Proteobacteria	1	Human feces; Human stool	Indirect association between microbiota composition and metabolites measured in host biospecimen
Archaea	Euryarchaeota	1	Human feces; Human	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	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Urine	Detected and Quantified	0.5	0	1	umol/mmol creatinine	Adult (>18 years old)	Both	Prostate Cancer	HMDB	19212411
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Colorectal cancer	HMDB	25037050
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Colorectal Cancer	HMDB	27015276
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Urine	Detected and Quantified	0.5	0.0	1.0	umol/mmol creatinine	Adult (>18 years old)	Both	Prostate Cancer	HMDB	19212411
Human Intestine	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified					Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified					Adult (>18 years old)	Both	Normal	HMDB	29808030
Human Blood	Detected but not Quantified								HMDB

External Links

HMDB ID

HMDB0001015

DrugBank ID

DB04464

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022372

KNApSAcK ID

Not Available

Chemspider ID

388809

KEGG Compound ID

C03145

BioCyc ID

N-FORMYLMETHIONINE

BiGG ID

Not Available

Wikipedia Link

Formylmethionine

METLIN ID

Not Available

PubChem Compound

439750

PDB ID

Not Available

ChEBI ID

16552

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Sherriff RM, Broom MF, Chadwick VS: Isolation and purification of N-formylmethionine aminopeptidase from rat intestine. Biochim Biophys Acta. 1992 Mar 12;1119(3):275-80. doi: 10.1016/0167-4838(92)90214-x. [PubMed:1547272 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for N-Formyl-L-methionine (MMDBc0000560)

MOL for #<Metabolite:0x00007fa4d8036798>

3D MOL for #<Metabolite:0x00007fa4d8036798>

3D SDF for #<Metabolite:0x00007fa4d8036798>

3D-SDF for #<Metabolite:0x00007fa4d8036798>

PDB for #<Metabolite:0x00007fa4d8036798>

3D PDB for #<Metabolite:0x00007fa4d8036798>

SMILES for #<Metabolite:0x00007fa4d8036798>

INCHI for #<Metabolite:0x00007fa4d8036798>

Structure for #<Metabolite:0x00007fa4d8036798>

3D Structure for #<Metabolite:0x00007fa4d8036798>