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Showing metabocard for Iodomethane (HMDB0253530)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2021-09-11 12:12:27 UTC
Update Date2021-09-26 23:06:48 UTC
HMDB IDHMDB0253530
Secondary Accession NumbersNone
Metabolite Identification
Common NameIodomethane
Descriptioniodomethane, also known as CH3I or MeI, belongs to the class of organic compounds known as halomethanes. These are organic compounds in which at least one of the four hydrogen atoms of methane (CH4) are replaced by halogen atoms. iodomethane is possibly neutral. Commercial samples may be stabilized by copper or silver wire. Unfortunately, it has a high equivalent weight: one mole of methyl iodide weighs almost three times as much as one mole of methyl chloride. For example, it can be used for the methylation of carboxylic acids or phenols:In these examples, the base (K2CO3 or Li2CO3) removes the acidic proton to form the carboxylate or phenoxide anion, which serves as the nucleophile in the SN2 substitution. This compound has been identified in human blood as reported by (PMID: 31557052 ). Iodomethane is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Iodomethane 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 HMDB0253530 (Iodomethane)


  Mrv0541 05031418282D          

  2  1  0  0  0  0            999 V2000
    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 I   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
M  END
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3D MOL for HMDB0253530 (Iodomethane)

HMDB0253530
     RDKit          3D
Iodomethane
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.1990   -0.0103   -0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9298   -0.0354    0.0204 I   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6115   -0.0341    1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5082    0.9532   -0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6111   -0.8735   -0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
M  END
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3D SDF for HMDB0253530 (Iodomethane)


  Mrv0541 05031418282D          

  2  1  0  0  0  0            999 V2000
    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 I   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0253530

> <DATABASE_NAME>
hmdb

> <SMILES>
CI

> <INCHI_IDENTIFIER>
InChI=1S/CH3I/c1-2/h1H3

> <INCHI_KEY>
INQOMBQAUSQDDS-UHFFFAOYSA-N

> <FORMULA>
CH3I

> <MOLECULAR_WEIGHT>
141.939

> <EXACT_MASS>
141.927943516

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
7.431846675210221

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
iodomethane

> <ALOGPS_LOGP>
1.20

> <JCHEM_LOGP>
1.5555657386666668

> <ALOGPS_LOGS>
-1.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0

> <JCHEM_REFRACTIVITY>
19.4953

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.09e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methyl iodide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0253530 (Iodomethane)

HMDB0253530
     RDKit          3D
Iodomethane
  5  4  0  0  0  0  0  0  0  0999 V2000
   -0.1990   -0.0103   -0.0130 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9298   -0.0354    0.0204 I   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6115   -0.0341    1.0214 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5082    0.9532   -0.4630 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6111   -0.8735   -0.5658 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
  1  4  1  0
  1  5  1  0
M  END
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PDB for HMDB0253530 (Iodomethane)

HEADER    PROTEIN                                 03-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  I   UNK     0       0.000   0.000   0.000  0.00  0.00           I+0
CONECT    1    2                                                            
CONECT    2    1                                                            
MASTER        0    0    0    0    0    0    0    0    2    0    2    0
END
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3D PDB for HMDB0253530 (Iodomethane)

COMPND    HMDB0253530
HETATM    1  C1  UNL     1      -0.199  -0.010  -0.013  1.00  0.00           C  
HETATM    2  I1  UNL     1       1.930  -0.035   0.020  1.00  0.00           I  
HETATM    3  H1  UNL     1      -0.611  -0.034   1.021  1.00  0.00           H  
HETATM    4  H2  UNL     1      -0.508   0.953  -0.463  1.00  0.00           H  
HETATM    5  H3  UNL     1      -0.611  -0.873  -0.566  1.00  0.00           H  
CONECT    1    2    3    4    5
END
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SMILES for HMDB0253530 (Iodomethane)

CI
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INCHI for HMDB0253530 (Iodomethane)

InChI=1S/CH3I/c1-2/h1H3
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View in JSmolView Stereo Labels
Synonyms
ValueSource
CH3IChEBI
IodmethanChEBI
Jod-methanChEBI
MeIChEBI
Methyl iodideChEBI
MethyliodidChEBI
MethyljodidChEBI
MonoiodmethanChEBI
MonoiodomethaneChEBI
Iodomethane-D3MeSH
Methyl iodide, 131I-labeledMeSH
Methyl iodide, 13C-labeledMeSH
Methyl iodide, 132I-labeledMeSH
Methyl iodide, 14C-labeledMeSH
Methyl iodide, 2H-labeledMeSH
Methyl iodide, 11C-labeledMeSH
Chemical FormulaCH3I
Average Molecular Weight141.939
Monoisotopic Molecular Weight141.927943516
IUPAC Nameiodomethane
Traditional Namemethyl iodide
CAS Registry NumberNot Available
SMILES
CI
InChI Identifier
InChI=1S/CH3I/c1-2/h1H3
InChI KeyINQOMBQAUSQDDS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as halomethanes. These are organic compounds in which at least one of the four hydrogen atoms of methane (CH4) are replaced by halogen atoms.
KingdomOrganic compounds
Super ClassOrganohalogen compounds
ClassAlkyl halides
Sub ClassHalomethanes
Direct ParentHalomethanes
Alternative Parents
Substituents
  • Halomethane
  • Hydrocarbon derivative
  • Organoiodide
  • Alkyl iodide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological location
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
logP1.2ALOGPS
logP1.56ChemAxon
logS-1.1ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity19.5 m³·mol⁻¹ChemAxon
Polarizability7.43 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]+119.26530932474
DeepCCS[M-H]-117.36930932474
DeepCCS[M-2H]-152.67630932474
DeepCCS[M+Na]+127.07130932474
AllCCS[M+H]+143.332859911
AllCCS[M+H-H2O]+139.232859911
AllCCS[M+NH4]+147.132859911
AllCCS[M+Na]+148.232859911
AllCCS[M-H]-289.332859911
AllCCS[M+Na-2H]-299.832859911
AllCCS[M+HCOO]-311.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
IodomethaneCI782.4Standard polar33892256
IodomethaneCI502.1Standard non polar33892256
IodomethaneCI512.8Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Iodomethane GC-MS (Non-derivatized) - 70eV, Positivesplash10-0006-0900000000-ea3aaf00c92fc8aa36272021-09-24Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Iodomethane GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 10V, Positive-QTOFsplash10-0006-0900000000-dfbfdbf31e4565f5245d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 20V, Positive-QTOFsplash10-0006-0900000000-dfbfdbf31e4565f5245d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 40V, Positive-QTOFsplash10-0006-0900000000-dfbfdbf31e4565f5245d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 10V, Negative-QTOFsplash10-0006-0900000000-68d07110dc8f8af9a84c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 20V, Negative-QTOFsplash10-0006-0900000000-68d07110dc8f8af9a84c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 40V, Negative-QTOFsplash10-0006-0900000000-68d07110dc8f8af9a84c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 10V, Positive-QTOFsplash10-0006-0900000000-21a3c005cce1a764951e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 20V, Positive-QTOFsplash10-0006-0900000000-21a3c005cce1a764951e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 40V, Positive-QTOFsplash10-0006-0900000000-21a3c005cce1a764951e2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 10V, Negative-QTOFsplash10-0006-0900000000-d0849183500c49313df92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 20V, Negative-QTOFsplash10-0006-0900000000-d0849183500c49313df92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Iodomethane 40V, Negative-QTOFsplash10-0006-0900000000-d0849183500c49313df92021-10-12Wishart LabView Spectrum
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 IDC18448
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkIodomethane
METLIN IDNot Available
PubChem Compound6328
PDB IDNot Available
ChEBI ID39282
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 ]