Hmdb loader
Survey

Showing metabocard for Thiocyanate (HMDB0001453)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
enzymes (3) Show 3 proteins
Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2020-10-09 21:01:44 UTC
HMDB IDHMDB0001453
Secondary Accession Numbers
  • HMDB01453
Metabolite Identification
Common NameThiocyanate
DescriptionThiocyanate is analogous to the cyanate ion, [OCN]-, wherein oxygen is replaced by sulfur. [SCN]- is one of the pseudohalogens, due to the similarity of its reactions to that of halide ions. Thiocyanate was formerly known as rhodanide (from a Greek word for rose) because of the red color of its complexes with iron. Thiocyanates are typically colorless. Cyanide ions can react with cystine to yield thicocyanate. This reaction occurs to a slight extent even in neutral solution, but is more pronounced in alkaline solutions of cystine. In addition to this non-enzymatic route, cyanide produced in vivo can be converted in part to thiocyanate by sulfur transferase systems. The thiocyanate ion can be oxidized at acid pH by hydrogen peroxide to generate sulfate and cyanide. The reaction is catalyzed by hemoglobin acting as a peroxidase. Thiocyanate is analogous to the cyanate ion, [OCN]-, wherein oxygen is replaced by sulfur. [SCN]- is one of the pseudohalogens, due to the similarity of its reactions to that of halide ions. Thiocyanate was formerly known as rhodanide (from a Greek word for rose) because of the red color of its complexes with iron. Thiocyanates are typically colorless. Cyanide ions can react with cystine to yield thicocyanate. This reaction occurs to a slight extent even in neutral solution, but is more pronounced in alkaline solutions of cystine. In addition to this non-enzymatic route, cyanide produced in vivo can be converted in part to thiocyanate by sulfur transferase systems. The thiocyanate ion can be oxidized at acid pH by hydrogen peroxide to generate sulfate and cyanide. The reaction is catalyzed by hemoglobin acting as a peroxidase. A study shows that thiocyanate has a protective effect in lung in cystic fibrosis, and an anti-inflammatory effect in arterial endothelial cells, a neuronal cell line, and a pancreatic beta cell line (PMID: 19918082 ). Thiocyanate has been identified as a uremic toxin according to the European Uremic Toxin Working Group (PMID: 22626821 ).
Structure
Data?1594316081
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0001453 (Thiocyanate)


  Mrv1652304202019272D          

  3  2  0  0  0  0            999 V2000
    2.9425   -2.2688    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7675   -2.2688    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1175   -2.2688    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
  3  1  1  0  0  0  0
A    1
C
M  CHG  1   3  -1
M  END
Download

3D MOL for HMDB0001453 (Thiocyanate)

HMDB0001453
     RDKit          3D
Thiocyanate
  3  2  0  0  0  0  0  0  0  0999 V2000
   -1.3621   -0.8387    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2060   -0.7004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5681   -0.4899    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
M  CHG  1   3  -1
M  END
Download

3D SDF for HMDB0001453 (Thiocyanate)


  Mrv1652304202019272D          

  3  2  0  0  0  0            999 V2000
    2.9425   -2.2688    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7675   -2.2688    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1175   -2.2688    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
  2  1  3  0  0  0  0
  3  1  1  0  0  0  0
A    1
C
M  CHG  1   3  -1
M  END
> <DATABASE_ID>
HMDB0001453

> <DATABASE_NAME>
hmdb

> <SMILES>
[S-]C#N

> <INCHI_IDENTIFIER>
InChI=1S/CHNS/c2-1-3/h3H/p-1

> <INCHI_KEY>
ZMZDMBWJUHKJPS-UHFFFAOYSA-M

> <FORMULA>
CNS

> <MOLECULAR_WEIGHT>
58.082

> <EXACT_MASS>
57.975144695

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
3

> <JCHEM_AVERAGE_POLARIZABILITY>
4.748552853899978

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cyanosulfanide

> <ALOGPS_LOGP>
0.22

> <JCHEM_LOGP>
0.5057528946666666

> <ALOGPS_LOGS>
-0.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.49709613151900633

> <JCHEM_POLAR_SURFACE_AREA>
23.79

> <JCHEM_REFRACTIVITY>
16.089399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.15e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
thiocyanate

> <JCHEM_VEBER_RULE>
1

$$$$
Download

3D-SDF for HMDB0001453 (Thiocyanate)

HMDB0001453
     RDKit          3D
Thiocyanate
  3  2  0  0  0  0  0  0  0  0999 V2000
   -1.3621   -0.8387    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2060   -0.7004    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5681   -0.4899    0.0000 S   0  0  0  0  0  1  0  0  0  0  0  0
  1  2  3  0
  2  3  1  0
M  CHG  1   3  -1
M  END
Download

PDB for HMDB0001453 (Thiocyanate)

HEADER    PROTEIN                                 20-APR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-20         0                                  
HETATM    1  C   UNK     0       5.493  -4.235   0.000  0.00  0.00           C+0
HETATM    2  N   UNK     0       7.033  -4.235   0.000  0.00  0.00           N+0
HETATM    3  S   UNK     0       3.953  -4.235   0.000  0.00  0.00           S-1
CONECT    1    2    3                                                       
CONECT    2    1                                                            
CONECT    3    1                                                            
MASTER        0    0    0    0    0    0    0    0    3    0    4    0
END
Download

3D PDB for HMDB0001453 (Thiocyanate)

COMPND    HMDB0001453
HETATM    1  N1  UNL     1      -1.362  -0.839   0.000  1.00  0.00           N  
HETATM    2  C1  UNL     1      -0.206  -0.700   0.000  1.00  0.00           C  
HETATM    3  S1  UNL     1       1.568  -0.490   0.000  1.00  0.00           S1-
CONECT    1    2    2    2
CONECT    2    3
END
Download

SMILES for HMDB0001453 (Thiocyanate)

[S-]C#N
Download

INCHI for HMDB0001453 (Thiocyanate)

InChI=1S/CHNS/c2-1-3/h3H/p-1
Download
View in JSmolView Stereo Labels
Synonyms
ValueSource
[S-C#N](-)ChEBI
N#C-S(-)ChEBI
RhodanidChEBI
RhodanideChEBI
SCN(-)ChEBI
THIOCYANATE ionChEBI
Thiocyanate ion (1-)ChEBI
ThiozyanatChEBI
THIOCYANic acid ionGenerator
Thiocyanic acid ion (1-)Generator
Thiocyanic acidGenerator
SCNHMDB
Ammonium sulfocyanateHMDB
HSCNHMDB
Hydrogen thiocyanateHMDB
NitridosulfanidocarbonHMDB
Silver thiocyanate agscnHMDB
Thallium thiocyanateHMDB
ThiocyanidHMDB
Weedazol TLHMDB
Thiocyanogen ((SCN)2(1-))MeSH, HMDB
Thiocyanate ion (2-)MeSH, HMDB
Chemical FormulaCNS
Average Molecular Weight58.082
Monoisotopic Molecular Weight57.975144695
IUPAC Namecyanosulfanide
Traditional Namethiocyanate
CAS Registry Number302-04-5
SMILES
[S-]C#N
InChI Identifier
InChI=1S/CHNS/c2-1-3/h3H/p-1
InChI KeyZMZDMBWJUHKJPS-UHFFFAOYSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as thiocyanates. These are salts or esters of thiocyanic acid, with the general formula RSC#N (R=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganosulfur compounds
ClassThiocyanates
Sub ClassNot Available
Direct ParentThiocyanates
Alternative Parents
Substituents
  • Thiocyanate
  • Organic nitrogen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Organic anion
  • 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
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 Solubility41.5 g/LALOGPS
logP0.22ALOGPS
logP0.51ChemAxon
logS-0.26ALOGPS
pKa (Strongest Acidic)0.5ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count1ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area23.79 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity16.09 m³·mol⁻¹ChemAxon
Polarizability4.75 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]+112.82130932474
DeepCCS[M-H]-111.00730932474
DeepCCS[M-2H]-146.20230932474
DeepCCS[M+Na]+119.94130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Thiocyanate[S-]C#N1128.7Standard polar33892256
Thiocyanate[S-]C#N566.8Standard non polar33892256
Thiocyanate[S-]C#N593.0Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyanate Quattro_QQQ 10V, Negative-QTOF (Annotated)splash10-0a4i-9000000000-afccae6819a2082a3b0e2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyanate Quattro_QQQ 25V, Negative-QTOF (Annotated)splash10-0a4i-9000000000-f7f42d61861dc8b47e0a2012-07-24HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Thiocyanate Quattro_QQQ 40V, Negative-QTOF (Annotated)splash10-0a4i-9000000000-d0c4694dff8128c82e832012-07-24HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 10V, Positive-QTOFsplash10-0a4i-9000000000-96a5deef504fc8cb30522016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 20V, Positive-QTOFsplash10-0a4i-9000000000-3714ea8b8485698022fe2016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 40V, Positive-QTOFsplash10-0a4i-9000000000-a4aa9bc6ab8c5ca45d182016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 10V, Negative-QTOFsplash10-0a4l-9000000000-3e068a4808fd5db992f02016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 20V, Negative-QTOFsplash10-052f-9000000000-5b443ccd8993bc2f93252016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 40V, Negative-QTOFsplash10-052f-9000000000-626420c56c66b85a0f642016-09-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 10V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 20V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Thiocyanate 40V, Negative-QTOFsplash10-0a4i-9000000000-286b63d3516de7d14a122021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Mitochondria
Biospecimen Locations
  • Blood
  • Cerebrospinal Fluid (CSF)
  • Feces
  • Saliva
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified30.7 +/- 28.8 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified59.8 +/- 26.1 uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
BloodDetected and Quantified4.99 +/- 1.03 uMAdult (>18 years old)BothNormal details
Cerebrospinal Fluid (CSF)Detected and Quantified27.6 (5.2-50.0) uMAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
SalivaDetected and Quantified661 (293-1029) uMAdult (>18 years old)BothNormal details
UrineDetected and Quantified1.840-5.140 umol/mmol creatinineNot SpecifiedBothNormal details
UrineDetected and Quantified4.61 (0.0 - 6.58) umol/mmol creatinineAdult (>18 years old)BothNormal
    • Geigy Scientific ...
 details
UrineDetected and Quantified0.00284 (0.00261-0.00310) umol/mmol creatinineAdult (>18 years old)Not SpecifiedNormal details
UrineDetected and Quantified0.00273 (0.00247-0.00300) umol/mmol creatinineChildren (1-13 years old)Not SpecifiedNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified32.02 +/- 2.93 uMAdult (>18 years old)Bothuremia details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Ulcerative colitis		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Crohn's disease 		details
UrineDetected and Quantified4.6 umol/mmol creatinineAdult (>18 years old)FemaleBeta-mercaptolactate-cysteine Disulfiduria details
Associated Disorders and Diseases
Disease References
Uremia
  1. Duranton F, Cohen G, De Smet R, Rodriguez M, Jankowski J, Vanholder R, Argiles A: Normal and pathologic concentrations of uremic toxins. J Am Soc Nephrol. 2012 Jul;23(7):1258-70. doi: 10.1681/ASN.2011121175. Epub 2012 May 24. [PubMed:22626821 ]
  2. Paul BD, Smith ML: Cyanide and thiocyanate in human saliva by gas chromatography-mass spectrometry. J Anal Toxicol. 2006 Oct;30(8):511-5. [PubMed:17132244 ]
  3. NA (2013). National Health and Nutrition Examination Survey (NHANES Survey) 2013. NA.
  4. (). Geigy Scientific Tables, 8th Rev edition, pp. 165-177. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.. .
  5. (). Geigy Scientific Tables, 8th Rev edition, pp. 80-82. Edited by C. Lentner, West Cadwell, N.J.: Medical education Div., Ciba-Geigy Corp., Basel, Switzerland c1981-1992.. .
Ulcerative colitis
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Crohn's disease
  1. De Preter V, Machiels K, Joossens M, Arijs I, Matthys C, Vermeire S, Rutgeerts P, Verbeke K: Faecal metabolite profiling identifies medium-chain fatty acids as discriminating compounds in IBD. Gut. 2015 Mar;64(3):447-58. doi: 10.1136/gutjnl-2013-306423. Epub 2014 May 8. [PubMed:24811995 ]
Beta-mercaptolactate-cysteine Disulfiduria
  1. Hannestad U, Martensson J, Sjodahl R, Sorbo B: 3-mercaptolactate cysteine disulfiduria: biochemical studies on affected and unaffected members of a family. Biochem Med. 1981 Aug;26(1):106-14. [PubMed:6945862 ]
Associated OMIM IDs
  • 266600 (Crohn's disease)
  • 249650 (Beta-mercaptolactate-cysteine Disulfiduria)
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB112173
KNApSAcK IDC00000137
Chemspider ID8961
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkThiocyanate
METLIN IDNot Available
PubChem Compound9322
PDB IDNot Available
ChEBI ID18022
Food Biomarker OntologyNot Available
VMH IDTCYNT
MarkerDB IDMDB00000327
Good Scents IDNot Available
References
Synthesis ReferenceLang, Konrad. Thiocyanate formation in the animal body. II. Biochemische Zeitschrift (1933), 263 262-7.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Paul BD, Smith ML: Cyanide and thiocyanate in human saliva by gas chromatography-mass spectrometry. J Anal Toxicol. 2006 Oct;30(8):511-5. [PubMed:17132244 ]
  2. Duranton F, Cohen G, De Smet R, Rodriguez M, Jankowski J, Vanholder R, Argiles A: Normal and pathologic concentrations of uremic toxins. J Am Soc Nephrol. 2012 Jul;23(7):1258-70. doi: 10.1681/ASN.2011121175. Epub 2012 May 24. [PubMed:22626821 ]
  3. Xu Y, Szep S, Lu Z: The antioxidant role of thiocyanate in the pathogenesis of cystic fibrosis and other inflammation-related diseases. Proc Natl Acad Sci U S A. 2009 Dec 1;106(48):20515-9. doi: 10.1073/pnas.0911412106. Epub 2009 Nov 16. [PubMed:19918082 ]

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
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