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Showing metabocard for Cyanide (HMDB0002084)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:35 UTC
Update Date2020-02-26 21:23:48 UTC
HMDB IDHMDB0002084
Secondary Accession Numbers
  • HMDB02084
Metabolite Identification
Common NameCyanide
DescriptionThe cyanide ion consists of a carbon triple bonded to a nitrogen. It readily reacts with hydrogen to form hydrogen cyanide gas, which has a faint almond-like smell. Most people can smell hydrogen cyanide; however, due to an apparent genetic trait, some individuals cannot. Cyanide gas (HCN) can be generated via combustion, including the exhaust of internal combustion engines, tobacco smoke, and especially some plastics derived from acrylonitrile (because of the latter effect, house fires can result in poisonings of the inhabitants). Cyanides are also produced by certain bacteria, fungi, and algae and are found in a number of foods and plants. Small amounts of cyanide can be found in apple seeds, mangoes and bitter almonds. Hydrocyanic acid (a solution of hydrogen cyanide in water) is present in freshly distilled bitter almond oil (2-4%) prior to its removal by precipitation as calcium ferrocyanide to give food quality oil. Hydrogen cyanide and most cyanide salts readily dissolve in water (or other biofluids) and exists in solution as the cyanide ion. Cyanide ions bind to the iron atom of the enzyme cytochrome c oxidase (also known as aa3) in the fourth complex in the mitochondrial membrane in the mitochondria of cells. The binding of cyanide to this cytochrome prevents transport of electrons from cytochrome c oxidase to oxygen. As a result, the electron transport chain is disrupted, meaning that the cell can no longer aerobically produce ATP for energy. Tissues that mainly depend on aerobic respiration, such as the central nervous system and the heart, are particularly affected. Because of its respiratory chain toxicity cyanide has been used as a poison many times throughout history. Its most infamous application was the use of hydrogen cyanide by the Nazi regime in Germany for mass murder in some gas chambers during the Holocaust. Hydrogen cyanide (with the historical common name of Prussic acid) is a colorless and highly volatile liquid that boils slightly above room temperature at 26 °C (78.8 °F). Hydrogen cyanide is weakly acidic and partly ionizes in solution to give the cyanide anion, CN-. The salts of hydrogen cyanide are known as cyanides. HCN is a highly valuable precursor to many chemical compounds ranging from polymers to pharmaceuticals. Hydrogen cyanide is a linear molecule, with a triple bond between carbon and nitrogen. It is a weak acid with a pKa of 9.2. A minor tautomer of HCN is HNC, hydrogen isocyanide.
Structure
Data?1582752228
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002084 (Cyanide)


  Mrv0541 02231219212D          

  2  1  0  0  0  0            999 V2000
    6.9987  -11.2613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8237  -11.2613    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
A    1
C
M  CHG  1   2  -1
M  END
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3D MOL for HMDB0002084 (Cyanide)

HMDB0002084
     RDKit          3D
Cyanide
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.5769    0.0000    0.0000 C   0  0  0  0  0  3  0  0  0  0  0  0
   -0.5769    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
M  CHG  1   1  -1
M  END
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3D SDF for HMDB0002084 (Cyanide)


  Mrv0541 02231219212D          

  2  1  0  0  0  0            999 V2000
    6.9987  -11.2613    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8237  -11.2613    0.0000 N   0  5  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
A    1
C
M  CHG  1   2  -1
M  END
> <DATABASE_ID>
HMDB0002084

> <DATABASE_NAME>
hmdb

> <SMILES>
C#[N-]

> <INCHI_IDENTIFIER>
InChI=1S/CHN/c1-2/h1H/q-1

> <INCHI_KEY>
ATBDVLSINHAXGY-UHFFFAOYSA-N

> <FORMULA>
CHN

> <MOLECULAR_WEIGHT>
27.0253

> <EXACT_MASS>
27.010899037

> <JCHEM_ACCEPTOR_COUNT>
0

> <JCHEM_AVERAGE_POLARIZABILITY>
2.3070561623346406

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
methylidyneazanidyl

> <ALOGPS_LOGP>
-0.74

> <ALOGPS_LOGS>
-1.06

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
7.0145

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.00e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
methylidyneazanidyl

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0002084 (Cyanide)

HMDB0002084
     RDKit          3D
Cyanide
  2  1  0  0  0  0  0  0  0  0999 V2000
    0.5769    0.0000    0.0000 C   0  0  0  0  0  3  0  0  0  0  0  0
   -0.5769    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
M  CHG  1   1  -1
M  END
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PDB for HMDB0002084 (Cyanide)

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      13.064 -21.021   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0      14.604 -21.021   0.000  0.00  0.00           N-1
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 HMDB0002084 (Cyanide)

COMPND    HMDB0002084
HETATM    1  C1  UNL     1       0.577   0.000   0.000  1.00  0.00           C1-
HETATM    2  N1  UNL     1      -0.577   0.000   0.000  1.00  0.00           N  
CONECT    1    2    2    2
END
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SMILES for HMDB0002084 (Cyanide)

C#[N-]
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INCHI for HMDB0002084 (Cyanide)

InChI=1S/CHN/c1-2/h1H/q-1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
Carbon nitride ionHMDB
Chuck norrisiumHMDB
Cyanide ionHMDB
Cyanide(1-) ionHMDB
CyanoHMDB
CyanureHMDB
IsocyanideHMDB
PrussiateHMDB
Chemical FormulaCHN
Average Molecular Weight27.0253
Monoisotopic Molecular Weight27.010899037
IUPAC Namemethylidyneazanidyl
Traditional Namemethylidyneazanidyl
CAS Registry Number57-12-5
SMILES
C#[N-]
InChI Identifier
InChI=1S/CHN/c1-2/h1H/q-1
InChI KeyATBDVLSINHAXGY-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as nitriles. Nitriles are compounds having the structure RC#N; thus C-substituted derivatives of hydrocyanic acid, HC#N.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassOrganic cyanides
Direct ParentNitriles
Alternative Parents
Substituents
  • Carbonitrile
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic anion
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility4 g/LALOGPS
logP-0.74ALOGPS
logS-1.1ALOGPS
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.79 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity7.01 m³·mol⁻¹ChemAxon
Polarizability2.31 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]+115.08330932474
DeepCCS[M-H]-113.34230932474
DeepCCS[M-2H]-148.92330932474
DeepCCS[M+Na]+122.78530932474

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified2.9 (0.0 - 11.7) uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified6.8 (1.3 - 19.4) uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
UrineDetected and Quantified0.01 (0.0052 - 15.13) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB006696
KNApSAcK IDC00007569
Chemspider ID5755
KEGG Compound IDC00177
BioCyc IDNot Available
BiGG ID34146
Wikipedia LinkCyanide
METLIN IDNot Available
PubChem Compound5975
PDB IDNot Available
ChEBI ID17514
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceFuruki, Masakazu; Moriguchi, Yuzo; Akakabe, Tethuro; Kitamura, Hiroyuki. Cyanide production with excess sludge incineration. Hyogo-kenritsu Kogai Kenkyusho Kenkyu Hokoku (1974), 6 31-5.
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. 3-mercaptopyruvate sulfurtransferase
General function:
Involved in thiosulfate sulfurtransferase activity
Specific function:
Transfer of a sulfur ion to cyanide or to other thiol compounds. Also has weak rhodanese activity. May have a role in cyanide degradation or in thiosulfate biosynthesis.
Gene Name:
MPST
Uniprot ID:
P25325
Molecular weight:
33178.15
Enzyme Details
2. Thiosulfate sulfurtransferase
General function:
Involved in thiosulfate sulfurtransferase activity
Specific function:
Formation of iron-sulfur complexes, cyanide detoxification or modification of sulfur-containing enzymes. Other thiol compounds, besides cyanide, can act as sulfur ion acceptors. Also has weak mercaptopyruvate sulfurtransferase (MST) activity (By similarity). Together with MRPL18, acts as a mitochondrial import factor for the cytosolic 5S rRNA. Only the nascent unfolded cytoplasmic form is able to bind to the 5S rRNA.
Gene Name:
TST
Uniprot ID:
Q16762
Molecular weight:
33428.69
Enzyme Details
3. Thiosulfate sulfurtransferase/rhodanese-like domain-containing protein 1
General function:
Inorganic ion transport and metabolism
Specific function:
Possible role in tumorgenesis
Gene Name:
TSTD1
Uniprot ID:
Q8NFU3
Molecular weight:
12530.1