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Showing metabocard for Methyl formate (HMDB0254588)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 13:58:00 UTC
Update Date2021-09-26 23:08:41 UTC
HMDB IDHMDB0254588
Secondary Accession NumbersNone
Metabolite Identification
Common NameMethyl formate
Descriptionmethyl formate, also known as HCO2CH3 or methyl methanoate, belongs to the class of organic compounds known as carboxylic acid esters. These are carboxylic acid derivatives in which the carbon atom from the carbonyl group is attached to an alkyl or an aryl moiety through an oxygen atom (forming an ester group). methyl formate is an extremely weak basic (essentially neutral) compound (based on its pKa). A formate ester resulting from the formal condensation of formic acid with methanol. This compound has been identified in human blood as reported by (PMID: 31557052 ). Methyl formate is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Methyl formate is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0254588 (Methyl formate)


  Mrv1533004191513182D          

  4  3  0  0  0  0            999 V2000
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
M  END
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3D MOL for HMDB0254588 (Methyl formate)

HMDB0254588
     RDKit          3D
Methyl formate
  8  7  0  0  0  0  0  0  0  0999 V2000
   -1.0542   -0.1235    0.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1987   -0.6771   -0.3201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3994   -0.0113   -0.1179 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    1.1382    0.4046 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9861    0.6345    0.8229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7350   -0.9280    0.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385    0.3893   -0.8473 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3670   -0.4222   -0.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
M  END
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3D SDF for HMDB0254588 (Methyl formate)


  Mrv1533004191513182D          

  4  3  0  0  0  0            999 V2000
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0254588

> <DATABASE_NAME>
hmdb

> <SMILES>
COC=O

> <INCHI_IDENTIFIER>
InChI=1S/C2H4O2/c1-4-2-3/h2H,1H3

> <INCHI_KEY>
TZIHFWKZFHZASV-UHFFFAOYSA-N

> <FORMULA>
C2H4O2

> <MOLECULAR_WEIGHT>
60.052

> <EXACT_MASS>
60.021129369

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
8

> <JCHEM_AVERAGE_POLARIZABILITY>
5.324618058492563

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methyl formate

> <ALOGPS_LOGP>
-0.31

> <JCHEM_LOGP>
-0.1261503663333334

> <ALOGPS_LOGS>
0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-6.80776767317914

> <JCHEM_POLAR_SURFACE_AREA>
26.3

> <JCHEM_REFRACTIVITY>
12.9223

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.98e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl formate

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0254588 (Methyl formate)

HMDB0254588
     RDKit          3D
Methyl formate
  8  7  0  0  0  0  0  0  0  0999 V2000
   -1.0542   -0.1235    0.0317 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1987   -0.6771   -0.3201 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3994   -0.0113   -0.1179 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3486    1.1382    0.4046 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9861    0.6345    0.8229 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7350   -0.9280    0.4081 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5385    0.3893   -0.8473 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3670   -0.4222   -0.3820 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  1  5  1  0
  1  6  1  0
  1  7  1  0
  3  8  1  0
M  END
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PDB for HMDB0254588 (Methyl formate)

HEADER    PROTEIN                                 19-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   19-APR-15         0                                  
HETATM    1  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       2.310  -1.334   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3                                                            
MASTER        0    0    0    0    0    0    0    0    4    0    6    0
END
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3D PDB for HMDB0254588 (Methyl formate)

COMPND    HMDB0254588
HETATM    1  C1  UNL     1      -1.054  -0.123   0.032  1.00  0.00           C  
HETATM    2  O1  UNL     1       0.199  -0.677  -0.320  1.00  0.00           O  
HETATM    3  C2  UNL     1       1.399  -0.011  -0.118  1.00  0.00           C  
HETATM    4  O2  UNL     1       1.349   1.138   0.405  1.00  0.00           O  
HETATM    5  H1  UNL     1      -0.986   0.634   0.823  1.00  0.00           H  
HETATM    6  H2  UNL     1      -1.735  -0.928   0.408  1.00  0.00           H  
HETATM    7  H3  UNL     1      -1.538   0.389  -0.847  1.00  0.00           H  
HETATM    8  H4  UNL     1       2.367  -0.422  -0.382  1.00  0.00           H  
CONECT    1    2    5    6    7
CONECT    2    3
CONECT    3    4    4    8
END
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SMILES for HMDB0254588 (Methyl formate)

COC=O
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INCHI for HMDB0254588 (Methyl formate)

InChI=1S/C2H4O2/c1-4-2-3/h2H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Formiate de methyleChEBI
Formic acid methyl esterChEBI
HCO2CH3ChEBI
HCOOCH3ChEBI
Methanoic acid methyl esterChEBI
Methyl methanoateChEBI
MethylformiatChEBI
R-611ChEBI
Formiic acid de methyleGenerator
Formate methyl esterGenerator
Methanoate methyl esterGenerator
Methyl methanoic acidGenerator
Methyl formic acidGenerator
Methyl formate, formic-18O-acid-O-methyl-labeledMeSH
Methyl formate, 18O-methyl ester-labeledMeSH
Methyl formate, hydrideMeSH
Chemical FormulaC2H4O2
Average Molecular Weight60.052
Monoisotopic Molecular Weight60.021129369
IUPAC Namemethyl formate
Traditional Namemethyl formate
CAS Registry NumberNot Available
SMILES
COC=O
InChI Identifier
InChI=1S/C2H4O2/c1-4-2-3/h2H,1H3
InChI KeyTZIHFWKZFHZASV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as carboxylic acid esters. These are carboxylic acid derivatives in which the carbon atom from the carbonyl group is attached to an alkyl or an aryl moiety through an oxygen atom (forming an ester group).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acid derivatives
Direct ParentCarboxylic acid esters
Alternative Parents
Substituents
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-0.31ALOGPS
logP-0.13ChemAxon
logS0.82ALOGPS
pKa (Strongest Basic)-6.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area26.3 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity12.92 m³·mol⁻¹ChemAxon
Polarizability5.32 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+118.18630932474
DeepCCS[M-H]-116.3330932474
DeepCCS[M-2H]-151.63130932474
DeepCCS[M+Na]+125.65230932474
AllCCS[M+H]+123.132859911
AllCCS[M+H-H2O]+118.632859911
AllCCS[M+NH4]+127.232859911
AllCCS[M+Na]+128.532859911
AllCCS[M-H]-140.332859911
AllCCS[M+Na-2H]-147.232859911
AllCCS[M+HCOO]-154.832859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20228.8292 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.96 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid942.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid364.2 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid139.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid277.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid69.7 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid264.1 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid329.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)325.6 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid632.2 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid147.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid768.3 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid220.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid282.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate613.3 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA291.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water202.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Methyl formateCOC=O741.4Standard polar33892256
Methyl formateCOC=O384.1Standard non polar33892256
Methyl formateCOC=O506.6Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkMethyl formate
METLIN IDNot Available
PubChem Compound7865
PDB IDNot Available
ChEBI ID77699
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]