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Showing metabocard for N-Formyl-L-methionine (HMDB0001015)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:24 UTC
HMDB IDHMDB0001015
Secondary Accession Numbers
  • HMDB01015
Metabolite Identification
Common NameN-Formyl-L-methionine
DescriptionN-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
Data?1676999724
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001015 (N-Formyl-L-methionine)

  Mrv1652303062020122D          

 11 10  0  0  0  0            999 V2000
 9999.2903 9999.9804    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.004810000.3927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7202 9999.9804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.433610000.3927    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
10002.1490 9999.9804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2903 9999.1561    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.0048 9998.7425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7202 9999.1561    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.575710000.3927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8609 9999.9804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.575710001.2174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  6  0  0  0
  1  9  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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
Download

3D MOL for HMDB0001015 (N-Formyl-L-methionine)

HMDB0001015
     RDKit          3D
N-Formyl-L-methionine
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.4584   -0.5206   -0.8202 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5656    1.0286   -0.9549 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1114    1.0543    0.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1214    0.0309   -0.3172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0763   -0.0072    0.5694 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9768   -1.0428    0.0299 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2906   -2.1577    0.8258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8124   -2.2627    1.9679 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8221    1.2596    0.6789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0381    1.3351    0.2811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831    2.4158    1.2021 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5357   -0.8600    0.2349 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4987   -0.3394   -1.2040 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9573   -1.3019   -1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3904    0.8615    1.2025 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6458    2.0681    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1596    0.2824   -1.3706 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5927   -0.9816   -0.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7555   -0.2860    1.5940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3539   -0.9236   -0.9188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9411   -2.9165    0.4490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3679    3.2638    0.6539 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  5  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  1
  6 20  1  0
  7 21  1  0
 11 22  1  0
M  END
Download

3D SDF for HMDB0001015 (N-Formyl-L-methionine)

  Mrv1652303062020122D          

 11 10  0  0  0  0            999 V2000
 9999.2903 9999.9804    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
10000.004810000.3927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7202 9999.9804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10001.433610000.3927    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
10002.1490 9999.9804    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2903 9999.1561    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
10000.0048 9998.7425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.7202 9999.1561    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.575710000.3927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.8609 9999.9804    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9998.575710001.2174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  6  1  6  0  0  0
  1  9  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
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001015

> <DATABASE_NAME>
hmdb

> <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

> <FORMULA>
C6H11NO3S

> <MOLECULAR_WEIGHT>
177.221

> <EXACT_MASS>
177.045963913

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
17.587295351677458

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S)-2-formamido-4-(methylsulfanyl)butanoic acid

> <ALOGPS_LOGP>
-0.61

> <JCHEM_LOGP>
-0.1571350413333333

> <ALOGPS_LOGS>
-1.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.896452545211904

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.92771597559532

> <JCHEM_PKA_STRONGEST_BASIC>
-1.4392999868293233

> <JCHEM_POLAR_SURFACE_AREA>
66.4

> <JCHEM_REFRACTIVITY>
42.539300000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.75e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
N-formylmethionine

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0001015 (N-Formyl-L-methionine)

HMDB0001015
     RDKit          3D
N-Formyl-L-methionine
 22 21  0  0  0  0  0  0  0  0999 V2000
    3.4584   -0.5206   -0.8202 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5656    1.0286   -0.9549 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1114    1.0543    0.1537 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1214    0.0309   -0.3172 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0763   -0.0072    0.5694 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.9768   -1.0428    0.0299 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2906   -2.1577    0.8258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8124   -2.2627    1.9679 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8221    1.2596    0.6789 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0381    1.3351    0.2811 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2831    2.4158    1.2021 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5357   -0.8600    0.2349 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4987   -0.3394   -1.2040 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9573   -1.3019   -1.4008 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3904    0.8615    1.2025 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6458    2.0681    0.1037 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1596    0.2824   -1.3706 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5927   -0.9816   -0.3134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7555   -0.2860    1.5940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3539   -0.9236   -0.9188 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9411   -2.9165    0.4490 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3679    3.2638    0.6539 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  2  0
  5  9  1  0
  9 10  2  0
  9 11  1  0
  1 12  1  0
  1 13  1  0
  1 14  1  0
  3 15  1  0
  3 16  1  0
  4 17  1  0
  4 18  1  0
  5 19  1  1
  6 20  1  0
  7 21  1  0
 11 22  1  0
M  END
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PDB for HMDB0001015 (N-Formyl-L-methionine)

HEADER    PROTEIN                                 06-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAR-20         0                                  
HETATM    1  C   UNK     0    8665.3428666.630   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0    8666.6768667.400   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0    8668.0118666.630   0.000  0.00  0.00           C+0
HETATM    4  S   UNK     0    8669.3438667.400   0.000  0.00  0.00           S+0
HETATM    5  C   UNK     0    8670.6788666.630   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0    8665.3428665.091   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0    8666.6768664.319   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0    8668.0118665.091   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0    8664.0088667.400   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0    8662.6748666.630   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8664.0088668.939   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4                                                            
CONECT    6    1    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7                                                            
CONECT    9    1   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   20    0
END
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3D PDB for HMDB0001015 (N-Formyl-L-methionine)

COMPND    HMDB0001015
HETATM    1  C1  UNL     1       3.458  -0.521  -0.820  1.00  0.00           C  
HETATM    2  S1  UNL     1       2.566   1.029  -0.955  1.00  0.00           S  
HETATM    3  C2  UNL     1       1.111   1.054   0.154  1.00  0.00           C  
HETATM    4  C3  UNL     1       0.121   0.031  -0.317  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.076  -0.007   0.569  1.00  0.00           C  
HETATM    6  N1  UNL     1      -1.977  -1.043   0.030  1.00  0.00           N  
HETATM    7  C5  UNL     1      -2.291  -2.158   0.826  1.00  0.00           C  
HETATM    8  O1  UNL     1      -1.812  -2.263   1.968  1.00  0.00           O  
HETATM    9  C6  UNL     1      -1.822   1.260   0.679  1.00  0.00           C  
HETATM   10  O2  UNL     1      -3.038   1.335   0.281  1.00  0.00           O  
HETATM   11  O3  UNL     1      -1.283   2.416   1.202  1.00  0.00           O  
HETATM   12  H1  UNL     1       3.536  -0.860   0.235  1.00  0.00           H  
HETATM   13  H2  UNL     1       4.499  -0.339  -1.204  1.00  0.00           H  
HETATM   14  H3  UNL     1       2.957  -1.302  -1.401  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.390   0.862   1.203  1.00  0.00           H  
HETATM   16  H5  UNL     1       0.646   2.068   0.104  1.00  0.00           H  
HETATM   17  H6  UNL     1      -0.160   0.282  -1.371  1.00  0.00           H  
HETATM   18  H7  UNL     1       0.593  -0.982  -0.313  1.00  0.00           H  
HETATM   19  H8  UNL     1      -0.756  -0.286   1.594  1.00  0.00           H  
HETATM   20  H9  UNL     1      -2.354  -0.924  -0.919  1.00  0.00           H  
HETATM   21  H10 UNL     1      -2.941  -2.916   0.449  1.00  0.00           H  
HETATM   22  H11 UNL     1      -1.368   3.264   0.654  1.00  0.00           H  
CONECT    1    2   12   13   14
CONECT    2    3
CONECT    3    4   15   16
CONECT    4    5   17   18
CONECT    5    6    9   19
CONECT    6    7   20
CONECT    7    8    8   21
CONECT    9   10   10   11
CONECT   11   22
END
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SMILES for HMDB0001015 (N-Formyl-L-methionine)

CSCC[C@H](NC=O)C(O)=O
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INCHI for HMDB0001015 (N-Formyl-L-methionine)

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
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
(2S)-2-(Formylamino)-4-(methylthio)butanoic acidChEBI
Formyl-methionineChEBI
N-FormylmethionineChEBI
(2S)-2-(Formylamino)-4-(methylthio)butanoateGenerator
Formylmethionine, NHMDB
N FormylmethionineHMDB
N-Formyl-L-methionineKEGG
Chemical FormulaC6H11NO3S
Average Molecular Weight177.221
Monoisotopic Molecular Weight177.045963913
IUPAC Name(2S)-2-formamido-4-(methylsulfanyl)butanoic acid
Traditional NameN-formylmethionine
CAS Registry Number4289-98-9
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 KeyPYUSHNKNPOHWEZ-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.
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassAmino acids, peptides, and analogues
Direct ParentMethionine 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 FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Baker140.73330932474
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Intestine
  • Placenta
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
UrineDetected and Quantified0.5 (0.0-1.0) umol/mmol creatinineAdult (>18 years old)Both
Prostate Cancer		 details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  2. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Prostate cancer
  1. Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Associated OMIM IDs
DrugBank IDDB04464
Phenol Explorer Compound IDNot Available
FooDB IDFDB022372
KNApSAcK IDNot Available
Chemspider ID388809
KEGG Compound IDC03145
BioCyc IDN-FORMYLMETHIONINE
BiGG IDNot Available
Wikipedia LinkFormylmethionine
METLIN IDNot Available
PubChem Compound439750
PDB IDNot Available
ChEBI ID16552
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceMilligan D L; Koshland D E Jr The amino terminus of the aspartate chemoreceptor is formylmethionine. The Journal of biological chemistry (1990), 265(8), 4455-60.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. 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. [PubMed:1547272 ]
  2. 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 ]