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Showing metabocard for Hydrogen cyanide (HMDB0060292)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
enzymes (2) Show 2 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-09 21:16:27 UTC
Update Date2023-02-21 17:29:50 UTC
HMDB IDHMDB0060292
Secondary Accession Numbers
  • HMDB60292
Metabolite Identification
Common NameHydrogen cyanide
DescriptionHydrogen cyanide, also known as cyanide or HCN, 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. Hydrogen cyanide exists in all living organisms, ranging from bacteria to humans. Hydrogen cyanide is found, on average, in the highest concentration within a few different foods, such as almonds (Prunus dulcis), flaxseeds (Linum usitatissimum), and cassavas (Manihot esculenta) and in a lower concentration in european plums (Prunus domestica) and common buckwheats (Fagopyrum esculentum). Hydrogen cyanide has also been detected, but not quantified in, several different foods, such as eddoes (Colocasia antiquorum), turnips (Brassica rapa var. rapa), pasta, deerberries (Vaccinium stamineum), and pepper (spice). This could make hydrogen cyanide a potential biomarker for the consumption of these foods. Hydrogen cyanide is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Hydrogen cyanide.
Structure
Data?1677000590
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0060292 (Hydrogen cyanide)


  Mrv1652309042000402D          

  2  1  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
M  END
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3D MOL for HMDB0060292 (Hydrogen cyanide)

HMDB0060292
     RDKit          3D
Hydrogen cyanide
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0304    0.6854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0401    0.2772    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0097    1.0393    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  1  3  1  0
M  END
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3D SDF for HMDB0060292 (Hydrogen cyanide)


  Mrv1652309042000402D          

  2  1  0  0  0  0            999 V2000
    0.8250    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0060292

> <DATABASE_NAME>
hmdb

> <SMILES>
C#N

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

> <INCHI_KEY>
LELOWRISYMNNSU-UHFFFAOYSA-N

> <FORMULA>
CHN

> <MOLECULAR_WEIGHT>
27.0253

> <EXACT_MASS>
27.010899037

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
2.307056162334641

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
formonitrile

> <ALOGPS_LOGP>
-0.65

> <JCHEM_LOGP>
-0.34619831566666665

> <ALOGPS_LOGS>
-0.92

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.499999999999998

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
7.0145

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.26e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
hydrogen cyanide

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0060292 (Hydrogen cyanide)

HMDB0060292
     RDKit          3D
Hydrogen cyanide
  3  2  0  0  0  0  0  0  0  0999 V2000
   -0.0304    0.6854    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0401    0.2772    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0097    1.0393    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  3  0
  1  3  1  0
M  END
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PDB for HMDB0060292 (Hydrogen cyanide)

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  C   UNK     0       1.540   0.000   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+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 HMDB0060292 (Hydrogen cyanide)

COMPND    HMDB0060292
HETATM    1  C1  UNL     1      -0.030   0.685   0.000  1.00  0.00           C  
HETATM    2  N1  UNL     1       1.040   0.277   0.000  1.00  0.00           N  
HETATM    3  H1  UNL     1      -1.010   1.039   0.000  1.00  0.00           H  
CONECT    1    2    2    2    3
END
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SMILES for HMDB0060292 (Hydrogen cyanide)

C#N
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INCHI for HMDB0060292 (Hydrogen cyanide)

InChI=1S/CHN/c1-2/h1H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
[CHN]ChEBI
BlausaeureChEBI
CyanwasserstoffChEBI
FormonitrileChEBI
HCNChEBI
Hydrocyanic acidChEBI
CyanideKegg
HydrocyanateGenerator
Zyklon bHMDB
Cyanide, hydrogenHMDB
Acid, hydrocyanicHMDB
Chemical FormulaCHN
Average Molecular Weight27.0253
Monoisotopic Molecular Weight27.010899037
IUPAC Nameformonitrile
Traditional Namehydrogen cyanide
CAS Registry Number74-90-8
SMILES
C#N
InChI Identifier
InChI=1S/CHN/c1-2/h1H
InChI KeyLELOWRISYMNNSU-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
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting Point5.00 °C. @ 0.00 mm HgThe Good Scents Company Information System
Boiling Point79.00 °C. @ 0.00 mm HgThe Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (exp)The Good Scents Company Information System
LogP-0.250The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility3.26 g/LALOGPS
logP-0.65ALOGPS
logP-0.35ChemAxon
logS-0.92ALOGPS
pKa (Strongest Acidic)9.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count1ChemAxon
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 FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+110.60130932474
DeepCCS[M-H]-108.8530932474
DeepCCS[M-2H]-144.01330932474
DeepCCS[M+Na]+117.34930932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202210.2649 minutes33406817
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid1023.0 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid456.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid203.2 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid368.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid207.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid337.8 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 Acid459.4 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)581.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid732.0 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid214.8 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid807.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid309.7 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid388.3 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate716.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA426.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water284.9 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Hydrogen cyanideC#N968.3Standard polar33892256
Hydrogen cyanideC#N236.3Standard non polar33892256
Hydrogen cyanideC#N223.1Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
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 IDFDB014486
KNApSAcK IDC00007569
Chemspider ID748
KEGG Compound IDC01326
BioCyc IDHCN
BiGG IDNot Available
Wikipedia LinkHydrogen_cyanide
METLIN IDNot Available
PubChem Compound768
PDB IDNot Available
ChEBI ID18407
Food Biomarker OntologyNot Available
VMH IDCYAN
MarkerDB IDNot Available
Good Scents IDrw1027341
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bolling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO: A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. [PubMed:23455439 ]

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
Reactions
3-Mercaptopyruvic acid + Hydrogen cyanide → Pyruvic acid + Thiocyanatedetails
Thiosulfate + Hydrogen cyanide → Sulfite + Thiocyanatedetails
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
Reactions
Thiosulfate + Hydrogen cyanide → Sulfite + Thiocyanatedetails
Hydrogen cyanide + 3-Mercaptopyruvic acid → Thiocyanate + Pyruvic aciddetails