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Showing NP-Card for N-Formyl-L-methionine (NP0001032)

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Record Information
Version2.0
Created at2005-11-16 15:48:42 UTC
Updated at2024-09-03 04:22:28 UTC
NP-MRD IDNP0001032
Natural Product DOIhttps://doi.org/10.57994/2872
Secondary Accession NumbersNone
Natural Product 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
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MOLSDFPDBSMILESInChI

MOL for NP0001032 (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
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3D MOL for NP0001032 (N-Formyl-L-methionine)

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3D SDF for NP0001032 (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>
NP0001032

> <DATABASE_NAME>
NP-MRD

> <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

$$$$

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3D-SDF for NP0001032 (N-Formyl-L-methionine)
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PDB for NP0001032 (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 NP0001032 (N-Formyl-L-methionine)
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SMILES for NP0001032 (N-Formyl-L-methionine)
CSCC[C@H](NC=O)C(O)=O
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INCHI for NP0001032 (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 JSmol
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 Mass177.2210 Da
Monoisotopic Mass177.04596 Da
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-/m1/s1
InChI KeyPYUSHNKNPOHWEZ-RXMQYKEDSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
HSQC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-18View Spectrum
COSY NMR[1H, 1H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-18View Spectrum
HMBC NMR[1H, 13C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-18View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-18View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-18View Spectrum
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-18View Spectrum
Species
Species of Origin
Species NameSourceReference
Anas platyrhynchos
Anatidae
Anser anser
Bison bison
Bos taurus
Bos taurus X Bison bison
Bubalus bubalis
Capra aegagrus hircus
Cervidae
Cervus canadensis
Columba
Columbidae
Dromaius novaehollandiae
Equus caballus
Gallus gallus
Lagopus muta
Leporidae
Lepus timidus
Melanitta fusca
Meleagris gallopavo
Numida meleagris
Odocoileus
Oryctolagus
Ovis aries
Phasianidae
Phasianus colchicus
Struthio camelus
Sus scrofa
Sus scrofa domestica
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
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility9.75 g/LALOGPS
logP-0.61ALOGPS
logP-0.16ChemAxon
logS-1.3ALOGPS
pKa (Strongest Acidic)3.93ChemAxon
pKa (Strongest Basic)-1.4ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area66.4 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity42.54 m³·mol⁻¹ChemAxon
Polarizability17.59 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001015  
DrugBank IDDB04464  
Phenol Explorer Compound IDNot Available
FoodDB IDFDB022372  
KNApSAcK IDNot Available
Chemspider ID5363142  
KEGG Compound IDC03145  
BioCyc IDN-FORMYLMETHIONINE  
BiGG IDNot Available
Wikipedia LinkFormylmethionine  
METLIN IDNot Available
PubChem Compound439750  
PDB IDNot Available
ChEBI ID16552  
Good Scents IDNot Available
References
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  ]