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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2006-05-22 14:17:55 UTC
Update Date2020-11-09 23:16:54 UTC
HMDB IDHMDB0002497
Secondary Accession Numbers
  • HMDB02497
Metabolite Identification
Common NameGlycochenodeoxycholate-3-sulfate
DescriptionGlycochenodeoxycholate-3-sulfate, also known as 3-sulfO-gcdca or GCDCS, belongs to the class of organic compounds known as glycinated bile acids and derivatives. Glycinated bile acids and derivatives are compounds with a structure characterized by the presence of a glycine linked to a bile acid skeleton. Glycochenodeoxycholate-3-sulfate is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1582752250
Synonyms
ValueSource
3-SulfO-gcdcaChEBI
GCDCSChEBI
Glycochenodeoxycholate-3-sulphateChEBI
3-SulphO-gcdcaGenerator
Glycochenodeoxycholic acid-3-sulfuric acidGenerator
Glycochenodeoxycholic acid-3-sulphuric acidGenerator
Glycochenodeoxycholic acid 3-sulfateHMDB
Glycochenodeoxycholic acid 3-sulphateHMDB
Glycochenodeoxycholic acid 3a-sulfateHMDB
Glycochenodeoxycholic acid 3a-sulphateHMDB
SulfoglycochenodeoxycholateHMDB
SulphoglycochenodeoxycholateHMDB
Sulphoglycochenodeoxycholic acidHMDB
Glycochenodeoxycholate-3-sulfateChEBI
Chemical FormulaC26H43NO8S
Average Molecular Weight529.687
Monoisotopic Molecular Weight529.270938047
IUPAC Name2-[(4R)-4-[(1S,2S,5R,7R,9R,10R,11S,14R,15R)-9-hydroxy-2,15-dimethyl-5-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido]acetic acid
Traditional Name[(4R)-4-[(1S,2S,5R,7R,9R,10R,11S,14R,15R)-9-hydroxy-2,15-dimethyl-5-(sulfooxy)tetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido]acetic acid
CAS Registry Number67030-54-0
SMILES
[H][C@@]1(CC[C@@]2([H])[C@]3([H])[C@H](O)C[C@]4([H])C[C@@H](CC[C@]4(C)[C@@]3([H])CC[C@]12C)OS(O)(=O)=O)[C@H](C)CCC(=O)NCC(O)=O
InChI Identifier
InChI=1S/C26H43NO8S/c1-15(4-7-22(29)27-14-23(30)31)18-5-6-19-24-20(9-11-26(18,19)3)25(2)10-8-17(35-36(32,33)34)12-16(25)13-21(24)28/h15-21,24,28H,4-14H2,1-3H3,(H,27,29)(H,30,31)(H,32,33,34)/t15-,16+,17-,18-,19+,20+,21-,24+,25+,26-/m1/s1
InChI KeyDKXXSIJHWWVNMO-GYPHWSFCSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as glycinated bile acids and derivatives. Glycinated bile acids and derivatives are compounds with a structure characterized by the presence of a glycine linked to a bile acid skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassBile acids, alcohols and derivatives
Direct ParentGlycinated bile acids and derivatives
Alternative Parents
Substituents
  • Glycinated bile acid
  • Hydroxy bile acid, alcohol, or derivatives
  • Monohydroxy bile acid, alcohol, or derivatives
  • Sulfated steroid skeleton
  • Hydroxysteroid
  • 7-hydroxysteroid
  • N-acyl-alpha-amino acid
  • N-acyl-alpha amino acid or derivatives
  • Alpha-amino acid or derivatives
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Sulfuric acid ester
  • Alkyl sulfate
  • Sulfuric acid monoester
  • Sulfate-ester
  • Organic sulfuric acid or derivatives
  • Cyclic alcohol
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Monocarboxylic acid or derivatives
  • Carbonyl group
  • Organic oxygen compound
  • Alcohol
  • Organopnictogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Biological location:

Source:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.0074 g/LALOGPS
logP0.21ALOGPS
logP1.13ChemAxon
logS-4.9ALOGPS
pKa (Strongest Acidic)-1.5ChemAxon
pKa (Strongest Basic)-0.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area150.23 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity132.07 m³·mol⁻¹ChemAxon
Polarizability57.72 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0ly6-0385980000-5995781cc4339ad4d582Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positivesplash10-0ab9-6011149000-2f25d614455105937729Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03e9-4000890000-a76b0d05c81b7bd6a04cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0059-9002800000-914d9b4365cc1961b88aSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-9005300000-213b06bd15d0fc90e9b5Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000490000-677a58b1c1864daa52b8Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-008a-3000920000-f2cab07a2ae7567da387Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00di-9101100000-02088e18627c221a62efSpectrum
Biological Properties
Cellular Locations
  • Extracellular
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Hepatocellular carcinoma
details
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Liver Cirrhosis
details
Associated Disorders and Diseases
Disease References
Hepatocellular carcinoma
  1. Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai TH, Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K: Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta. 2012 Sep 19;743:90-100. doi: 10.1016/j.aca.2012.07.013. Epub 2012 Jul 20. [PubMed:22882828 ]
Cirrhosis
  1. Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai TH, Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K: Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta. 2012 Sep 19;743:90-100. doi: 10.1016/j.aca.2012.07.013. Epub 2012 Jul 20. [PubMed:22882828 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023015
KNApSAcK IDNot Available
Chemspider ID19991236
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID6702
PubChem Compound21125002
PDB IDNot Available
ChEBI ID72733
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Ressom HW, Xiao JF, Tuli L, Varghese RS, Zhou B, Tsai TH, Ranjbar MR, Zhao Y, Wang J, Di Poto C, Cheema AK, Tadesse MG, Goldman R, Shetty K: Utilization of metabolomics to identify serum biomarkers for hepatocellular carcinoma in patients with liver cirrhosis. Anal Chim Acta. 2012 Sep 19;743:90-100. doi: 10.1016/j.aca.2012.07.013. Epub 2012 Jul 20. [PubMed:22882828 ]

Enzymes

General function:
Involved in binding
Specific function:
Ileal protein which stimulates gastric acid and pepsinogen secretion. Seems to be able to bind to bile salts and bilirubins. Isoform 2 is essential for the survival of colon cancer cells to bile acid-induced apoptosis
Gene Name:
FABP6
Uniprot ID:
P51161
Molecular weight:
14371.2
References
  1. Kurz M, Brachvogel V, Matter H, Stengelin S, Thuring H, Kramer W: Insights into the bile acid transportation system: the human ileal lipid-binding protein-cholyltaurine complex and its comparison with homologous structures. Proteins. 2003 Feb 1;50(2):312-28. [PubMed:12486725 ]

Transporters

General function:
Involved in transporter activity
Specific function:
Mediates the Na(+)-independent transport of organic anions such as 17-beta-glucuronosyl estradiol, taurocholate, triiodothyronine (T3), leukotriene C4, dehydroepiandrosterone sulfate (DHEAS), methotrexate and sulfobromophthalein (BSP)
Gene Name:
SLCO1B3
Uniprot ID:
Q9NPD5
Molecular weight:
77402.2
General function:
Involved in transporter activity
Specific function:
Mediates the Na(+)-independent transport of organic anions such as pravastatin, taurocholate, methotrexate, dehydroepiandrosterone sulfate, 17-beta-glucuronosyl estradiol, estrone sulfate, prostaglandin E2, thromboxane B2, leukotriene C3, leukotriene E4, thyroxine and triiodothyronine. May play an important role in the clearance of bile acids and organic anions from the liver
Gene Name:
SLCO1B1
Uniprot ID:
Q9Y6L6
Molecular weight:
76448.0
References
  1. Michalski C, Cui Y, Nies AT, Nuessler AK, Neuhaus P, Zanger UM, Klein K, Eichelbaum M, Keppler D, Konig J: A naturally occurring mutation in the SLC21A6 gene causing impaired membrane localization of the hepatocyte uptake transporter. J Biol Chem. 2002 Nov 8;277(45):43058-63. Epub 2002 Aug 23. [PubMed:12196548 ]
General function:
Involved in ATP binding
Specific function:
May act as an inducible transporter in the biliary and intestinal excretion of organic anions. Acts as an alternative route for the export of bile acids and glucuronides from cholestatic hepatocytes
Gene Name:
ABCC3
Uniprot ID:
O15438
Molecular weight:
169341.1
General function:
Involved in ATP binding
Specific function:
Involved in the ATP-dependent secretion of bile salts into the canaliculus of hepatocytes
Gene Name:
ABCB11
Uniprot ID:
O95342
Molecular weight:
146405.8
General function:
Involved in bile acid:sodium symporter activity
Specific function:
Plays a critical role in the sodium-dependent reabsorption of bile acids from the lumen of the small intestine. Plays a key role in cholesterol metabolism
Gene Name:
SLC10A2
Uniprot ID:
Q12908
Molecular weight:
37697.4
References
  1. Kramer W, Girbig F, Glombik H, Corsiero D, Stengelin S, Weyland C: Identification of a ligand-binding site in the Na+/bile acid cotransporting protein from rabbit ileum. J Biol Chem. 2001 Sep 21;276(38):36020-7. Epub 2001 Jul 10. [PubMed:11447228 ]
General function:
Involved in bile acid:sodium symporter activity
Specific function:
The hepatic sodium/bile acid uptake system exhibits broad substrate specificity and transports various non-bile acid organic compounds as well. It is strictly dependent on the extracellular presence of sodium.
Gene Name:
SLC10A1
Uniprot ID:
Q14973
Molecular weight:
38118.64
General function:
Involved in transporter activity
Specific function:
Mediates the Na(+)-independent transport of organic anions such as sulfobromophthalein (BSP) and conjugated (taurocholate) and unconjugated (cholate) bile acids
Gene Name:
SLCO1A2
Uniprot ID:
P46721
Molecular weight:
74144.1
General function:
Involved in transporter activity
Specific function:
Mediates the Na(+)-independent transport of organic anions such as the thyroid hormones T3 (triiodo-L-thyronine), T4 (thyroxine) and rT3, and of estrone-3-sulfate and taurocholate
Gene Name:
SLCO4A1
Uniprot ID:
Q96BD0
Molecular weight:
77192.5