Showing metabocard for Hydrogen sulfide (MMDBc0000231)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:40:39 UTC
Update Date2024-09-27 17:21:06 UTC
Metabolite IDMMDBc0000231
Metabolite Identification
Common NameHydrogen sulfide
DescriptionHydrogen sulfide is a highly toxic and flammable gas. Because it is heavier than air it tends to accumulate at the bottom of poorly ventilated spaces. Although very pungent at first, it quickly deadens the sense of smell, so potential victims may be unaware of its presence until it is too late. H2S arises from virtually anywhere where elemental sulfur comes into contact with organic material, especially at high temperatures. Hydrogen sulfide is a covalent hydride chemically related to water (H2O) since oxygen and sulfur occur in the same periodic table group. It often results when bacteria break down organic matter in the absence of oxygen, such as in swamps, and sewers (alongside the process of anaerobic digestion). It also occurs in volcanic gases, natural gas and some well waters. It is also important to note that Hydrogen sulfide is a central participant in the sulfur cycle, the biogeochemical cycle of sulfur on Earth. As mentioned above, sulfur-reducing and sulfate-reducing bacteria derive energy from oxidizing hydrogen or organic molecules in the absence of oxygen by reducing sulfur or sulfate to hydrogen sulfide. Other bacteria liberate hydrogen sulfide from sulfur-containing amino acids. Several groups of bacteria can use hydrogen sulfide as fuel, oxidizing it to elemental sulfur or to sulfate by using oxygen or nitrate as oxidant. The purple sulfur bacteria and the green sulfur bacteria use hydrogen sulfide as electron donor in photosynthesis, thereby producing elemental sulfur. (In fact, this mode of photosynthesis is older than the mode of cyanobacteria, algae and plants which uses water as electron donor and liberates oxygen). Hydrogen sulfide can be found in Alcaligenes, Chromobacteriumn, Klebsiella, Proteus and Pseudomonas (PMID: 13061742 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x0000559d0532d0f0>


  Mrv1652309042000282D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x0000559d0532d0f0>

HMDB0003276
     RDKit          3D
Hydrogen sulfide
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0045    0.5475   -0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1492   -0.2722    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1447   -0.2753   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
M  END
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3D SDF for #<Metabolite:0x0000559d0532d0f0>


  Mrv1652309042000282D          

  1  0  0  0  0  0            999 V2000
    0.0000    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000231

> <DATABASE_NAME>
MIME

> <SMILES>
S

> <INCHI_IDENTIFIER>
InChI=1S/H2S/h1H2

> <INCHI_KEY>
RWSOTUBLDIXVET-UHFFFAOYSA-N

> <FORMULA>
H2S

> <MOLECULAR_WEIGHT>
34.081

> <EXACT_MASS>
33.987720754

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_ATOM_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
3.450817136572978

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
hydrogen sulfide

> <JCHEM_LOGP>
-0.03749999999999998

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_POLAR_SURFACE_AREA>
0.0

> <JCHEM_REFRACTIVITY>
7.3558

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
hydrogen sulfide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for #<Metabolite:0x0000559d0532d0f0>

HMDB0003276
     RDKit          3D
Hydrogen sulfide
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0045    0.5475   -0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.1492   -0.2722    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1447   -0.2753   -0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  1  3  1  0
M  END
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PDB for #<Metabolite:0x0000559d0532d0f0>

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  S   UNK     0       0.000   0.000   0.000  0.00  0.00           S+0
MASTER        0    0    0    0    0    0    0    0    1    0    0    0
END
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3D PDB for #<Metabolite:0x0000559d0532d0f0>

COMPND    HMDB0003276
HETATM    1  S1  UNL     1      -0.004   0.547  -0.000  1.00  0.00           S  
HETATM    2  H1  UNL     1       1.149  -0.272   0.000  1.00  0.00           H  
HETATM    3  H2  UNL     1      -1.145  -0.275  -0.000  1.00  0.00           H  
CONECT    1    2    3
END
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SMILES for #<Metabolite:0x0000559d0532d0f0>

S
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INCHI for #<Metabolite:0x0000559d0532d0f0>

InChI=1S/H2S/h1H2
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Synonyms
ValueSource
[SH2]ChEBI
Acide sulfhydriqueChEBI
Dihydrogen monosulfideChEBI
Dihydrogen sulfideChEBI
H2SChEBI
Hydrogen monosulfideChEBI
Hydrogen sulphideChEBI
Hydrogen-sulfideChEBI
Hydrogene sulfureChEBI
HYDROsulfURIC ACIDChEBI
SchwefelwasserstoffChEBI
SulfideChEBI
Sulfure d'hydrogeneChEBI
Acide sulphhydriqueGenerator
Dihydrogen monosulphideGenerator
Dihydrogen sulphideGenerator
Hydrogen monosulphideGenerator
Hydrogen-sulphideGenerator
Hydrogene sulphureGenerator
HYDROsulfateGenerator
HYDROsulphateGenerator
HYDROsulphuric acidGenerator
SulphideGenerator
Sulphure d'hydrogeneGenerator
Dihydrogen disulfideHMDB
HepatateHMDB
Hepatic acidHMDB
Hepatic gasHMDB
HydrosulfurateHMDB
Idrogeno solforatoHMDB
Sewer gasHMDB
SiarkowodorHMDB
Sour gasHMDB
Stink dAMPHMDB
Sulfur hydrideHMDB
Sulfur hydroxideHMDB
Sulfureted hydrogenHMDB
Sulfuretted hydrogenHMDB
ZwavelwaterstofHMDB
Sulfide, hydrogenHMDB
Hydrogen sulfide (H2(SX))HMDB
Hydrogen sulfide (H2S2)HMDB
Hydrogen sulfide (H2S3)HMDB
Molecular FormulaH2S
Average Mass34.081
Monoisotopic Mass33.987720754
IUPAC Namehydrogen sulfide
Traditional Namehydrogen sulfide
CAS Registry Number7783-06-4
SMILES
S
InChI Identifier
InChI=1S/H2S/h1H2
InChI KeyRWSOTUBLDIXVET-UHFFFAOYSA-N