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Showing metabocard for Methanol (HMDB0001875)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-02-23 13:09:54 UTC
Update Date2023-02-21 17:15:54 UTC
HMDB IDHMDB0001875
Secondary Accession Numbers
  • HMDB01875
Metabolite Identification
Common NameMethanol
DescriptionMethanol, also known as columbian spirit or CH3OH, belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl). The target of methanol in the eye is the retina, specifically the optic disk and optic nerve. Toxicity is due to the metabolic products of alcohol dehydrogenase (ADH) and aldehyde dehydrogenase. Methanol exists in all living organisms, ranging from bacteria to humans. Methanol is an alcoholic tasting compound. Outside of the human body, Methanol is found, on average, in the highest concentration within cow milk and sweet oranges. Methanol has also been detected, but not quantified in several different foods, such as prairie turnips, mountain yams, mentha (mint), watermelons, and pasta. Methanol is responsible for accidental, suicidal, and epidemic poisonings, resulting in death or permanent sequelae. Methanol is a potentially toxic compound. Visual disturbances develop between 18h to 48h after ingestion and range from mild photophobia and blurred vision to markedly reduced visual acuity and complete blindness. Methanol is metabolized to formaldehyde by alcohol dehydrogenase, then from that to formate by formaldehyde dehydrogenase, and then to carbon dioxide by limited H4 folate. It is the simplest alcohol, and is a light, volatile, colourless, flammable, poisonous liquid with a distinctive odor that is somewhat milder and sweeter than ethanol.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001875 (Methanol)

  Mrv1652309042000252D          

  2  1  0  0  0  0            999 V2000
    4.6887   -4.5100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5137   -4.5100    0.0000 O   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 HMDB0001875 (Methanol)

HMDB0001875
     RDKit          3D
Methanol
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.3814   -0.0326   -0.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9536   -0.4607   -0.1418 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007   -0.8826   -0.3845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5294    0.8782   -0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5951    0.2175    1.0489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5531    0.2803    0.1198 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
  2  6  1  0
M  END
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3D SDF for HMDB0001875 (Methanol)

  Mrv1652309042000252D          

  2  1  0  0  0  0            999 V2000
    4.6887   -4.5100    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5137   -4.5100    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001875

> <DATABASE_NAME>
hmdb

> <SMILES>
CO

> <INCHI_IDENTIFIER>
InChI=1S/CH4O/c1-2/h2H,1H3

> <INCHI_KEY>
OKKJLVBELUTLKV-UHFFFAOYSA-N

> <FORMULA>
CH4O

> <MOLECULAR_WEIGHT>
32.0419

> <EXACT_MASS>
32.02621475

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
3.3823377787776097

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methanol

> <ALOGPS_LOGP>
-1.38

> <JCHEM_LOGP>
-0.5185770686666668

> <ALOGPS_LOGS>
1.21

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
15.775593215075904

> <JCHEM_PKA_STRONGEST_BASIC>
-2.459555527725798

> <JCHEM_POLAR_SURFACE_AREA>
20.23

> <JCHEM_REFRACTIVITY>
8.2613

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.19e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methanol

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0001875 (Methanol)

HMDB0001875
     RDKit          3D
Methanol
  6  5  0  0  0  0  0  0  0  0999 V2000
   -0.3814   -0.0326   -0.0109 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9536   -0.4607   -0.1418 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0007   -0.8826   -0.3845 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5294    0.8782   -0.6315 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5951    0.2175    1.0489 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5531    0.2803    0.1198 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
  2  6  1  0
M  END
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PDB for HMDB0001875 (Methanol)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  C   UNK     0       8.752  -8.419   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      10.292  -8.419   0.000  0.00  0.00           O+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 HMDB0001875 (Methanol)

COMPND    HMDB0001875
HETATM    1  C1  UNL     1      -0.381  -0.033  -0.011  1.00  0.00           C  
HETATM    2  O1  UNL     1       0.954  -0.461  -0.142  1.00  0.00           O  
HETATM    3  H1  UNL     1      -1.001  -0.883  -0.384  1.00  0.00           H  
HETATM    4  H2  UNL     1      -0.529   0.878  -0.631  1.00  0.00           H  
HETATM    5  H3  UNL     1      -0.595   0.217   1.049  1.00  0.00           H  
HETATM    6  H4  UNL     1       1.553   0.280   0.120  1.00  0.00           H  
CONECT    1    2    3    4    5
CONECT    2    6
END
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SMILES for HMDB0001875 (Methanol)

CO
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INCHI for HMDB0001875 (Methanol)

InChI=1S/CH4O/c1-2/h2H,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaCH4O
Average Molecular Weight32.0419
Monoisotopic Molecular Weight32.02621475
IUPAC Namemethanol
Traditional Namemethanol
CAS Registry Number67-56-1
SMILES
CO
InChI Identifier
InChI=1S/CH4O/c1-2/h2H,1H3
InChI KeyOKKJLVBELUTLKV-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as primary alcohols. Primary alcohols are compounds comprising the primary alcohol functional group, with the general structure RCOH (R=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassAlcohols and polyols
Direct ParentPrimary alcohols
Alternative Parents
Substituents
  • Hydrocarbon derivative
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Health effectOrganoleptic effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationEnvironmental roleBiological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-97.6 °CNot Available
Boiling Point64.00 to 65.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility1000 mg/mL at 25 °CNot Available
LogP-0.77HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Lysosome
  • Endoplasmic reticulum
Biospecimen Locations
  • Blood
  • Breast Milk
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Adrenal Gland
  • Brain
  • Epidermis
  • Erythrocyte
  • Fibroblasts
  • Hair
  • Intestine
  • Kidney
  • Liver
  • Neuron
  • Pancreas
  • Platelet
  • Prostate
  • Skeletal Muscle
  • Spleen
  • Testis
Pathways
Normal Concentrations
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Alcoholism
  1. Jones AW, Lund M, Andersson E: Drinking drivers in Sweden who consume denatured alcohol preparations: an analytical-toxicological study. J Anal Toxicol. 1989 Jul-Aug;13(4):199-203. [PubMed:2779169 ]
  2. Jones AW, Helander A: Changes in the concentrations of ethanol, methanol and metabolites of serotonin in two successive urinary voids from drinking drivers. Forensic Sci Int. 1998 May 11;93(2-3):127-34. [PubMed:9717263 ]
  3. Jones AW, Lowinger H: Relationship between the concentration of ethanol and methanol in blood samples from Swedish drinking drivers. Forensic Sci Int. 1988 Jun;37(4):277-85. [PubMed:3410397 ]
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
  2. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Diarrhoea predominant irritable bowel syndrome
  1. Ahmed I, Greenwood R, Costello Bde L, Ratcliffe NM, Probert CS: An investigation of fecal volatile organic metabolites in irritable bowel syndrome. PLoS One. 2013;8(3):e58204. doi: 10.1371/journal.pone.0058204. Epub 2013 Mar 13. [PubMed:23516449 ]
Crohn's disease
  1. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Diverticular disease
  1. Tursi A, Mastromarino P, Capobianco D, Elisei W, Miccheli A, Capuani G, Tomassini A, Campagna G, Picchio M, Giorgetti G, Fabiocchi F, Brandimarte G: Assessment of Fecal Microbiota and Fecal Metabolome in Symptomatic Uncomplicated Diverticular Disease of the Colon. J Clin Gastroenterol. 2016 Oct;50 Suppl 1:S9-S12. doi: 10.1097/MCG.0000000000000626. [PubMed:27622378 ]
Rheumatoid arthritis
  1. Tie-juan ShaoZhi-xing HeZhi-jun XieHai-chang LiMei-jiao WangCheng-ping Wen. Characterization of ankylosing spondylitis and rheumatoid arthritis using 1H NMR-based metabolomics of human fecal extracts. Metabolomics. April 2016, 12:70 [Link]
Eosinophilic esophagitis
  1. Slae, M., Huynh, H., Wishart, D.S. (2014). Analysis of 30 normal pediatric urine samples via NMR spectroscopy (unpublished work). NA.
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB008124
KNApSAcK IDC00050480
Chemspider ID864
KEGG Compound IDC00132
BioCyc IDMETOH
BiGG ID33974
Wikipedia LinkMethanol
METLIN ID4201
PubChem Compound887
PDB IDNot Available
ChEBI ID17790
Food Biomarker OntologyNot Available
VMH IDMEOH
MarkerDB IDMDB00013443
Good Scents IDrw1259561
References
Synthesis ReferenceCummings, Donald Ray. Process for production of methanol from a methane gas stream. PCT Int. Appl. (2007), 21pp.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Lactoperoxidase
General function:
Involved in peroxidase activity
Specific function:
May contribute to airway host defense against infection.
Gene Name:
LPO
Uniprot ID:
P22079
Molecular weight:
70983.6
Enzyme Details
2. Peroxiredoxin-6
General function:
Involved in antioxidant activity
Specific function:
Involved in redox regulation of the cell. Can reduce H(2)O(2) and short chain organic, fatty acid, and phospholipid hydroperoxides. May play a role in the regulation of phospholipid turnover as well as in protection against oxidative injury.
Gene Name:
PRDX6
Uniprot ID:
P30041
Molecular weight:
25034.715
Reactions
Methanol + Hydrogen peroxide → Formaldehyde + Waterdetails
Enzyme Details
3. Myeloperoxidase
General function:
Involved in peroxidase activity
Specific function:
Part of the host defense system of polymorphonuclear leukocytes. It is responsible for microbicidal activity against a wide range of organisms. In the stimulated PMN, MPO catalyzes the production of hypohalous acids, primarily hypochlorous acid in physiologic situations, and other toxic intermediates that greatly enhance PMN microbicidal activity.
Gene Name:
MPO
Uniprot ID:
P05164
Molecular weight:
83867.71
Enzyme Details
4. Eosinophil peroxidase
General function:
Involved in peroxidase activity
Specific function:
Mediates tyrosine nitration of secondary granule proteins in mature resting eosinophils. Shows significant inhibitory activity towards Mycobacterium tuberculosis H37Rv by inducing bacterial fragmentation and lysis.
Gene Name:
EPX
Uniprot ID:
P11678
Molecular weight:
81039.5
Enzyme Details
5. Catalase
General function:
Involved in catalase activity
Specific function:
Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells including T-cells, B-cells, myeloid leukemia cells, melanoma cells, mastocytoma cells and normal and transformed fibroblast cells.
Gene Name:
CAT
Uniprot ID:
P04040
Molecular weight:
59755.82
Reactions
Methanol + Hydrogen peroxide → Formaldehyde + Waterdetails
Enzyme Details
6. Protein phosphatase methylesterase 1
General function:
Not Available
Specific function:
Demethylates proteins that have been reversibly carboxymethylated. Demethylates PPP2CB (in vitro) and PPP2CA. Binding to PPP2CA displaces the manganese ion and inactivates the enzyme.
Gene Name:
PPME1
Uniprot ID:
Q9Y570
Molecular weight:
43869.905
Reactions
[Phosphatase 2A protein]-leucine methyl ester + Water → [phosphatase 2A protein]-leucine + Methanoldetails