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Showing metabocard for Methane (HMDB0002714)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-05-22 15:12:05 UTC
Update Date2020-04-22 23:29:35 UTC
HMDB IDHMDB0002714
Secondary Accession Numbers
  • HMDB02714
Metabolite Identification
Common NameMethane
DescriptionMethane (CH4), is a gas produced by a group of colonic anaerobes, absorbed from the colon and excreted in expired air. As a result, breath CH4 excretion can be used as an indicator of the in situ activity of the methanogenic flora. All CH4 produced in human beings is a metabolic product of intestinal bacteria, and about 50% of CH4 produced in the gut is absorbed and excreted in expired air. Because there appears to be no catabolism of this gas by other colonic organisms or host cells, breath CH4 measurements provide a rapid, simple means of semi quantitatively assessing the ongoing in situ metabolism of the methanogenic flora. It could seem likely that the intracolonic activity of a variety of bacteria similarly might be assessed quantitatively via analysis of expired air. However, the application of this methodology has been confounded by the rapid catabolism of many volatile bacterial products by other bacteria or human tissue. A striking aspect of the studies of breath CH4 measurements is the enormous individual variations in the excretion of this gas. Virtually all children under 5 years of age and 66% of the adult population do not exhale appreciable quantities of CH4. The remaining 34% of the adult population has appreciable breath methane concentrations of up to 80 ppm (mean, 15.2 ppm; median, 11.8 ppm). On this basis the population can be divided into CH4 producers or nonproducers, although a more accurate term would be to define subjects as being low or high CH4 producers. The primary methanogen present in the human colon, Methanobrevibacter smithii, produces methane via a reaction that relies entirely on H2 produced by other organisms to reduce CO2 to CH4. Thus, breath CH4 concentrations might be expected to mirror breath H2 concentrations; however, the high levels of CH4 observed in the fasting state may result from H2 derived from endogenous rather than dietary substrates. A diverse assortment of conditions has been associated with a high prevalence of methane producers including diverticulosis, cystic fibrosis, high fasting serum cholesterol levels, encopresis in children, and aorto-iliac vascular disease, whereas obesity (measured as skin-fold thickness) was related inversely to methane production. The challenge that remains is to determine to what extent methanogens actively influence body physiology vs. simply serve as passive indicators of colonic function. (PMID: 16469670 , Clinical Gastroenterology and Hepatology Volume 4, Issue 2, February 2006, Pages 123-129). Methane can be found in Desulfovibrio, Methanobacterium, Methanobrevibacter, Methanococcus, Methanocorpusculum, Methanoculleus, Methanoflorens, Methanofollis, Methanogenium, Methanomicrobium, Methanopyrus, Methanoregula, Methanosaeta, Methanosarcina, Methanosphaera, Methanospirillium, Methanothermobacter (Wikipedia ).
Structure
Data?1582752254
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002714 (Methane)

297
  Mrv1652305271900202D          

  1  0  0  0  0  0            999 V2000
    3.3759    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for HMDB0002714 (Methane)

HMDB0002714
     RDKit          3D
Methane
  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0019   -0.0040   -0.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5395    0.7900   -0.5449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7017   -0.4724    0.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3967   -0.7808   -0.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8426    0.4672    0.5243 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
Download

3D SDF for HMDB0002714 (Methane)

297
  Mrv1652305271900202D          

  1  0  0  0  0  0            999 V2000
    3.3759    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002714

> <DATABASE_NAME>
hmdb

> <SMILES>
C

> <INCHI_IDENTIFIER>
InChI=1S/CH4/h1H4

> <INCHI_KEY>
VNWKTOKETHGBQD-UHFFFAOYSA-N

> <FORMULA>
CH4

> <MOLECULAR_WEIGHT>
16.0425

> <EXACT_MASS>
16.031300128

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
2.5910020514760492

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methane

> <ALOGPS_LOGP>
-1.31

> <JCHEM_LOGP>
1.0809229439999999

> <ALOGPS_LOGS>
1.08

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
6.3468

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
0.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methane

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0002714 (Methane)

HMDB0002714
     RDKit          3D
Methane
  5  4  0  0  0  0  0  0  0  0999 V2000
    0.0019   -0.0040   -0.0028 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5395    0.7900   -0.5449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7017   -0.4724    0.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3967   -0.7808   -0.6687 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8426    0.4672    0.5243 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
Download

PDB for HMDB0002714 (Methane)

HEADER    PROTEIN                                 27-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 297                                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-MAY-19         0                                  
HETATM    1  C   UNK     0       6.302   0.000   0.000  0.00  0.00           C+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
Download

3D PDB for HMDB0002714 (Methane)

COMPND    HMDB0002714
HETATM    1  C1  UNL     1       0.002  -0.004  -0.003  1.00  0.00           C  
HETATM    2  H1  UNL     1      -0.540   0.790  -0.545  1.00  0.00           H  
HETATM    3  H2  UNL     1      -0.702  -0.472   0.692  1.00  0.00           H  
HETATM    4  H3  UNL     1       0.397  -0.781  -0.669  1.00  0.00           H  
HETATM    5  H4  UNL     1       0.843   0.467   0.524  1.00  0.00           H  
CONECT    1    2    3    4    5
END
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SMILES for HMDB0002714 (Methane)

C
Download

INCHI for HMDB0002714 (Methane)

InChI=1S/CH4/h1H4
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
CH4ChEBI
Marsh gasChEBI
MetanoChEBI
MethanChEBI
Methyl hydrideChEBI
ActicarboneHMDB
AdsorbitHMDB
AnthrasorbHMDB
AquadagHMDB
AroflowHMDB
ArogenHMDB
ArotoneHMDB
ArovelHMDB
ArrowHMDB
AtlanticHMDB
BiogasHMDB
CancarbHMDB
CanesorbHMDB
CanlubHMDB
CarbeneHMDB
CarbodisHMDB
CarbolacHMDB
CarbometHMDB
CarboneHMDB
CarboniumHMDB
CarbonoHMDB
CarbosieveHMDB
CecarbonHMDB
CollocarbHMDB
ConductexHMDB
ContinexHMDB
CroflexHMDB
CrolacHMDB
DarcoHMDB
DegussaHMDB
ElectrographiteHMDB
ElftexHMDB
EssexHMDB
ExcelsiorHMDB
FarbrussHMDB
FectoHMDB
FiltrasorbHMDB
Fire dAMPHMDB
FlamrussHMDB
FurnalHMDB
FurnexHMDB
GastexHMDB
GrafoilHMDB
GrosafeHMDB
HuberHMDB
HumenegroHMDB
HydrodarcoHMDB
KohlenstoffHMDB
KorobonHMDB
KosminkHMDB
KosmobilHMDB
KosmolakHMDB
KosmosHMDB
KosmothermHMDB
KosmovarHMDB
LampblackHMDB
MagecolHMDB
MetanexHMDB
Methane in gaseus STateHMDB
MethyleneHMDB
MethylidyneHMDB
MicronexHMDB
ModulexHMDB
MolaccoHMDB
NeotexHMDB
NucharHMDB
PapyexHMDB
PelletexHMDB
PhilblackHMDB
PlumbagoHMDB
PrintexHMDB
R 50HMDB
RebonexHMDB
SchungiteHMDB
SevacarbHMDB
ShungiteHMDB
SpheronHMDB
StatexHMDB
SuperbaHMDB
ThermatomicHMDB
ThermaxHMDB
ThermblackHMDB
TinoliteHMDB
WatercarbHMDB
Chemical FormulaCH4
Average Molecular Weight16.0425
Monoisotopic Molecular Weight16.031300128
IUPAC Namemethane
Traditional Namemethane
CAS Registry Number74-82-8
SMILES
C
InChI Identifier
InChI=1S/CH4/h1H4
InChI KeyVNWKTOKETHGBQD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alkanes. These are acyclic branched or unbranched hydrocarbons having the general formula CnH2n+2 , and therefore consisting entirely of hydrogen atoms and saturated carbon atoms.
KingdomOrganic compounds
Super ClassHydrocarbons
ClassSaturated hydrocarbons
Sub ClassAlkanes
Direct ParentAlkanes
Alternative ParentsNot Available
Substituents
  • Acyclic alkane
  • Alkane
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleEnvironmental roleIndustrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-182.4 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility0.022 mg/mL at 25 °CNot Available
LogP1.09HANSCH,C ET AL. (1995)
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP-1.3ALOGPS
logP1.08ChemAxon
logS1.08ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity6.35 m³·mol⁻¹ChemAxon
Polarizability2.59 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.1416 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid262.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1243.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid526.7 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid223.1 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid418.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid258.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid416.8 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 Acid525.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)529.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid861.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid319.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1011.9 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid360.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid414.5 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate751.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA444.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water265.6 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
MethaneC692.5Standard polar33892256
MethaneC229.2Standard non polar33892256
MethaneC68.1Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Adipose Tissue
  • Fibroblasts
  • Intestine
  • Kidney
  • Liver
  • Platelet
  • Skeletal Muscle
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
UrineExpected but not QuantifiedNot QuantifiedNot AvailableNot AvailableNormal
      Not Available
 details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn's disease 		details
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Crohn's disease
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023051
KNApSAcK IDC00045198
Chemspider ID291
KEGG Compound IDC01438
BioCyc IDCH4
BiGG IDNot Available
Wikipedia LinkMethane
METLIN ID3190
PubChem Compound297
PDB IDNot Available
ChEBI ID16183
Food Biomarker OntologyNot Available
VMH IDCH4
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceTamaura, Yutaka. Method for manufacture of methane. Jpn. Kokai Tokkyo Koho (1994), 9 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Minh NH, Someya M, Minh TB, Kunisue T, Iwata H, Watanabe M, Tanabe S, Viet PH, Tuyen BC: Persistent organochlorine residues in human breast milk from Hanoi and Hochiminh City, Vietnam: contamination, accumulation kinetics and risk assessment for infants. Environ Pollut. 2004 Jun;129(3):431-41. [PubMed:15016464 ]
  2. Castelain P, Van Hummelen P, Deleener A, Kirsch-Volders M: Automated detection of cytochalasin-B blocked binucleated lymphocytes for scoring micronuclei. Mutagenesis. 1993 Jul;8(4):285-93. [PubMed:7690875 ]
  3. Rumessen JJ, Gudmand-Hoyer E: Fructans of chicory: intestinal transport and fermentation of different chain lengths and relation to fructose and sorbitol malabsorption. Am J Clin Nutr. 1998 Aug;68(2):357-64. [PubMed:9701194 ]
  4. Florin TH, Woods HJ: Inhibition of methanogenesis by human bile. Gut. 1995 Sep;37(3):418-21. [PubMed:7590441 ]
  5. Tsai WB, Shi Q, Grunkemeier JM, McFarland C, Horbett TA: Platelet adhesion to radiofrequency glow-discharge-deposited fluorocarbon polymers preadsorbed with selectively depleted plasmas show the primary role of fibrinogen. J Biomater Sci Polym Ed. 2004;15(7):817-40. [PubMed:15318794 ]
  6. Bernalier A, Willems A, Leclerc M, Rochet V, Collins MD: Ruminococcus hydrogenotrophicus sp. nov., a new H2/CO2-utilizing acetogenic bacterium isolated from human feces. Arch Microbiol. 1996 Sep;166(3):176-83. [PubMed:8703194 ]
  7. Ringvoll J, Nordstrand LM, Vagbo CB, Talstad V, Reite K, Aas PA, Lauritzen KH, Liabakk NB, Bjork A, Doughty RW, Falnes PO, Krokan HE, Klungland A: Repair deficient mice reveal mABH2 as the primary oxidative demethylase for repairing 1meA and 3meC lesions in DNA. EMBO J. 2006 May 17;25(10):2189-98. Epub 2006 Apr 27. [PubMed:16642038 ]
  8. Poyart C, Bursaux E, Freminet A, Bertin M: Interactions of short chain aliphatic hydrocarbons with human blood and haemoglobin A solutions. Biomedicine. 1976 Jul;25(6):224-7. [PubMed:963185 ]
  9. Rabot S, Viso M, Martin F, Blanquie JP, Popot F, Bensaada M, Vaissade P, Searby N, Szylit O: Effects of chair-restraint on gastrointestinal transit time and colonic fermentation in male rhesus monkey (Macaca mulatta). J Med Primatol. 1997 Aug;26(4):190-5. [PubMed:9416569 ]
  10. Kresimon J, Gruter UM, Hirner AV: HG/LT-GC/ICP-MS coupling for identification of metal(loid) species in human urine after fish consumption. Fresenius J Anal Chem. 2001 Nov;371(5):586-90. [PubMed:11767883 ]
  11. Nakamura M, Ueki S, Hara H, Arata T: Calcium structural transition of human cardiac troponin C in reconstituted muscle fibres as studied by site-directed spin labelling. J Mol Biol. 2005 Apr 22;348(1):127-37. [PubMed:15808858 ]
  12. Kayar SR, Miller TL, Wolin MJ, Aukhert EO, Axley MJ, Kiesow LA: Decompression sickness risk in rats by microbial removal of dissolved gas. Am J Physiol. 1998 Sep;275(3 Pt 2):R677-82. [PubMed:9728062 ]
  13. Chien YH, Bau DT, Jan KY: Nitric oxide inhibits DNA-adduct excision in nucleotide excision repair. Free Radic Biol Med. 2004 Apr 15;36(8):1011-7. [PubMed:15059641 ]
  14. Eastwood MA, Brydon WG, Anderson DM: The effects of dietary gum karaya (Sterculia) in man. Toxicol Lett. 1983 Jun;17(1-2):159-66. [PubMed:6623502 ]
  15. Supko JG, Malspeis L: Characterization of the urinary metabolites of merbarone in cancer patients. Drug Metab Dispos. 1991 Jan-Feb;19(1):263-73. [PubMed:1673412 ]
  16. Escobar R, Cano Pavon JM: Selective spectrophotometric determination of trace amounts of iron with di(2-pyridyl)-NN-di[(8-quinolyl)amino]methane: determination of iron in blood serum. Analyst. 1983 Jul;108(1288):821-6. [PubMed:6614500 ]
  17. Wolever TM, Fernandes J, Rao VA, Chiasson JL, Josse RG, Leiter LA: Positive methane-producing status associated with increased serum cholesterol in subjects with impaired glucose tolerance. Diabetes Care. 1995 Jul;18(7):1010-2. [PubMed:7555532 ]
  18. Masson P, Marnot B, Lombard JY, Morelis P: [Electrophoretic study of aged butyrylcholinesterase after inhibition by soman]. Biochimie. 1984 Mar;66(3):235-49. [PubMed:6331528 ]
  19. Sudaryanto A, Kunisue T, Tanabe S, Niida M, Hashim H: Persistent organochlorine compounds in human breast milk from mothers living in Penang and Kedah, Malaysia. Arch Environ Contam Toxicol. 2005 Oct;49(3):429-37. Epub 2005 Aug 24. [PubMed:16132420 ]
  20. Nagao M, Takatori T, Oono T, Iwase H, Iwadate K, Yamada Y, Nakajima M: Death due to a methane gas explosion in a tunnel on urban reclaimed land. Am J Forensic Med Pathol. 1997 Jun;18(2):135-9. [PubMed:9185928 ]
  21. Levitt MD, Furne JK, Kuskowski M, Ruddy J: Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements. Clin Gastroenterol Hepatol. 2006 Feb;4(2):123-9. [PubMed:16469670 ]