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Showing metabocard for Hydrogen (HMDB0001362)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
enzymes (1) Show 1 protein
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2006-08-16 13:52:05 UTC
Update Date2022-03-07 02:49:09 UTC
HMDB IDHMDB0001362
Secondary Accession Numbers
  • HMDB01362
Metabolite Identification
Common NameHydrogen
DescriptionHydrogen is a colorless, odorless, nonmetallic, tasteless, highly flammable diatomic gas with the molecular formula H2. With an atomic weight of 1.00794, hydrogen is the lightest element. Besides the common H1 isotope, hydrogen exists as the stable isotope Deuterium and the unstable, radioactive isotope Tritium. Hydrogen is the most abundant of the chemical elements, constituting roughly 75% of the universe's elemental mass. Hydrogen can form compounds with most elements and is present in water and most organic compounds. It plays a particularly important role in acid-base chemistry, in which many reactions involve the exchange of protons between soluble molecules. Oxidation of hydrogen, in the sense of removing its electron, formally gives H+, containing no electrons and a nucleus which is usually composed of one proton. That is why H+ is often called a proton. This species is central to discussion of acids. Under the Bronsted-Lowry theory, acids are proton donors, while bases are proton acceptors. A bare proton H+ cannot exist in solution because of its strong tendency to attach itself to atoms or molecules with electrons. However, the term 'proton' is used loosely to refer to positively charged or cationic hydrogen, denoted H+. H2 is a product of some types of anaerobic metabolism and is produced by several microorganisms, usually via reactions catalyzed by iron- or nickel-containing enzymes called hydrogenases. These enzymes catalyze the reversible redox reaction between H2 and its component two protons and two electrons. Creation of hydrogen gas occurs in the transfer of reducing equivalents produced during pyruvate fermentation to water. Hydrogen has been found to be a metabolite of Citrobacter, Cyanobacteria, Enterobacter, Halobacterium and Rhodobacteraceae (PMID: 28042989 ; PMID: 16371161 ) (https://www.insa.nic.in/writereaddata/UpLoadedFiles/PINSA/Vol51B_1985_2_Art16.pdf) (https://www.researchgate.net/publication/222428793_High_Hydrogen_Yield_from_a_Two-step_Process_of_Dark-_and_Photo-fermentation_of_Sucrose) (Tao, Y; Chen, Y; Wu, Y; He, Y; Zhou, Z (2007). "High hydrogen yield from a two-step process of dark- and photo-fermentation of sucrose". International Journal of Hydrogen Energy. 32 (2): 200-206).
Structure
Data?1582752195
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001362 (Hydrogen)


  Mrv1652309042000212D          

  2  1  0  0  0  0            999 V2000
   11.1056   -6.0445    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9306   -6.0445    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
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3D MOL for HMDB0001362 (Hydrogen)

HMDB0001362
     RDKit          3D
Hydrogen
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.3517    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3517    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
M  END
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3D SDF for HMDB0001362 (Hydrogen)


  Mrv1652309042000212D          

  2  1  0  0  0  0            999 V2000
   11.1056   -6.0445    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9306   -6.0445    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001362

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][H]

> <INCHI_IDENTIFIER>
InChI=1S/H2/h1H

> <INCHI_KEY>
UFHFLCQGNIYNRP-UHFFFAOYSA-N

> <FORMULA>
H2

> <MOLECULAR_WEIGHT>
2.0159

> <EXACT_MASS>
2.015650064

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
2

> <JCHEM_AVERAGE_POLARIZABILITY>
0.7414234180599918

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
dihydrogen

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
0.0

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
dihydrogen

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0001362 (Hydrogen)

HMDB0001362
     RDKit          3D
Hydrogen
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.3517    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3517    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
M  END
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PDB for HMDB0001362 (Hydrogen)

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  H   UNK     0      20.730 -11.283   0.000  0.00  0.00           H+0
HETATM    2  H   UNK     0      22.270 -11.283   0.000  0.00  0.00           H+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 HMDB0001362 (Hydrogen)

COMPND    HMDB0001362
HETATM    1  H1  UNL     1       0.352   0.000   0.000  1.00  0.00           H  
HETATM    2  H2  UNL     1      -0.352   0.000   0.000  1.00  0.00           H  
CONECT    1    2
END
Download

SMILES for HMDB0001362 (Hydrogen)

[H][H]
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INCHI for HMDB0001362 (Hydrogen)

InChI=1S/H2/h1H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
e 949ChEBI
e-949ChEBI
e949ChEBI
H2ChEBI
Molecular hydrogenChEBI
DihydrogenHMDB
Hydrogen gasHMDB
Hydrogen-1MeSH, HMDB
Hydrogen 1MeSH, HMDB
Chemical FormulaH2
Average Molecular Weight2.0159
Monoisotopic Molecular Weight2.015650064
IUPAC Namedihydrogen
Traditional Namedihydrogen
CAS Registry Number1333-74-0
SMILES
[H][H]
InChI Identifier
InChI=1S/H2/h1H
InChI KeyUFHFLCQGNIYNRP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of inorganic compounds known as other non-metal hydrides. These are inorganic compounds in which the heaviest atom bonded to a hydrogen atom is belongs to the class of 'other non-metals'.
KingdomInorganic compounds
Super ClassHomogeneous non-metal compounds
ClassOther non-metal organides
Sub ClassOther non-metal hydrides
Direct ParentOther non-metal hydrides
Alternative ParentsNot Available
Substituents
  • Other non-metal hydride
Molecular FrameworkNot Available
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-259.2 °CNot Available
Boiling Point-252.77 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility0.0016 mg/mL at 21 °CNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity0 m³·mol⁻¹ChemAxon
Polarizability0.74 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+110.64330932474
DeepCCS[M-H]-108.83530932474
DeepCCS[M-2H]-144.00930932474
DeepCCS[M+Na]+117.58830932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 20229.6203 minutes33406817
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid262.9 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid829.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid395.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid182.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid326.1 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid183.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid291.0 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 Acid370.6 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)528.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid609.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid153.5 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid709.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid264.0 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid346.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate647.7 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA350.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water271.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Hydrogen[H][H]356.5Standard polar33892256
Hydrogen[H][H]108.9Standard non polar33892256
Hydrogen[H][H]66.5Semi standard non polar33892256
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
  • Nucleus
  • Lysosome
  • Endoplasmic reticulum
  • Golgi apparatus
  • Peroxisome
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB016247
KNApSAcK IDC00023091
Chemspider ID762
KEGG Compound IDC00282
BioCyc IDHYDROGEN-MOLECULE
BiGG ID33778
Wikipedia LinkHydrogen
METLIN IDNot Available
PubChem Compound783
PDB IDNot Available
ChEBI ID18276
Food Biomarker OntologyNot Available
VMH IDH2
MarkerDB IDNot Available
Good Scents IDrw1250851
References
Synthesis ReferenceAit-Ichou, I.; Formenti, M.; Pommier, B.; Teichner, S. J. Photocatalytic dehydrogenation of isopropanol on platinum/titania catalysts. Journal of Catalysis (1985), 91(2), 293-307.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Asadi N, Zilouei H: Optimization of organosolv pretreatment of rice straw for enhanced biohydrogen production using Enterobacter aerogenes. Bioresour Technol. 2017 Mar;227:335-344. doi: 10.1016/j.biortech.2016.12.073. Epub 2016 Dec 23. [PubMed:28042989 ]
  2. Dutta D, De D, Chaudhuri S, Bhattacharya SK: Hydrogen production by Cyanobacteria. Microb Cell Fact. 2005 Dec 21;4:36. doi: 10.1186/1475-2859-4-36. [PubMed:16371161 ]

Enzymes

Enzyme Details
1. Voltage-gated hydrogen channel 1
General function:
Involved in ion channel activity
Specific function:
Mediates the voltage-dependent proton permeability of excitable membranes. Forms a proton-selective channel through which protons may pass in accordance with their electrochemical gradient. Proton efflux, accompanied by membrane depolarization, facilitates acute production of reactive oxygen species in phagocytosis
Gene Name:
HVCN1
Uniprot ID:
Q96D96
Molecular weight:
31682.9