Showing metabocard for Hydrogen (MMDBc0000188)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:39:06 UTC
Update Date2024-09-29 09:17:33 UTC
Metabolite IDMMDBc0000188
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
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f46df897ad8>


  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 #<Metabolite:0x00007f46df897ad8>

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 #<Metabolite:0x00007f46df897ad8>


  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>
MMDBc0000188

> <DATABASE_NAME>
MIME

> <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 #<Metabolite:0x00007f46df897ad8>

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 #<Metabolite:0x00007f46df897ad8>

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 #<Metabolite:0x00007f46df897ad8>

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
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SMILES for #<Metabolite:0x00007f46df897ad8>

[H][H]
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INCHI for #<Metabolite:0x00007f46df897ad8>

InChI=1S/H2/h1H
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Synonyms
ValueSource
e 949ChEBI
e-949ChEBI
e949ChEBI
H2ChEBI
Molecular hydrogenChEBI
DihydrogenHMDB
Hydrogen gasHMDB
Hydrogen-1MeSH, HMDB
Hydrogen 1MeSH, HMDB
Molecular FormulaH2
Average Mass2.0159
Monoisotopic Mass2.015650064
IUPAC Namedihydrogen
Traditional Namedihydrogen
CAS Registry Number1333-74-0
SMILES
[H][H]
InChI Identifier
InChI=1S/H2/h1H
InChI KeyUFHFLCQGNIYNRP-UHFFFAOYSA-N