Human Metabolome Database: Showing metabocard for Deoxycholic acid glycine conjugate (HMDB0000631)

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Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

enzymes (4) Show 4 proteins

Record Information

Version

4.0

Status

Detected and Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2020-02-26 21:22:25 UTC

HMDB ID

HMDB0000631

Secondary Accession Numbers

HMDB0004012
HMDB00631
HMDB04012

Metabolite Identification

Common Name

Deoxycholic acid glycine conjugate

Description

Deoxycholic acid glycine conjugate, or Deoxygcholylglycine, is an acyl glycine and a bile acid-glycine conjugate. It is a secondary bile acid produced by the action of enzymes existing in the microbial flora of the colonic environment. In hepatocytes, both primary and secondary bile acids undergo amino acid conjugation at the C-24 carboxylic acid on the side chain, and almost all bile acids in the bile duct therefore exist in a glycine conjugated form (PMID: 16949895 ). As a bile salt it acts as a detergent to solubilize fats for absorption and is itself absorbed. It is used as a cholagogue and choleretic.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
Deoxycholate glycine conjugate	Generator
Deoxycholic acid glycine conjugic acid	Generator
Deoxycholylglycine	HMDB
Deoxyglycocholate	HMDB
Deoxyglycocholic acid	HMDB
Glycodeoxycholate	HMDB
Glycodeoxycholic acid	HMDB
Glycodesoxycholate	HMDB
Glycodesoxycholic acid	HMDB
Glycyldeoxycholate	HMDB
Glycyldeoxycholic acid	HMDB
N-(3a,12a-Dihydroxy-5b-cholan-24-oyl)-glycine	HMDB
N-(Carboxymethyl)-3a,12a-dihydroxy-5b-cholan-24-amide	HMDB
Deoxycholate, glycine	HMDB
Acid, glycodeoxycholic	HMDB
Glycine deoxycholate	HMDB

Chemical Formula

C₂₆H₄₃NO₅

Average Molecular Weight

449.6233

Monoisotopic Molecular Weight

449.314123491

IUPAC Name

2-[(4R)-4-[(2S,5R,7R,14R,15R,16S)-5,16-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]pentanamido]acetic acid

Traditional Name

[(4R)-4-[(2S,5R,7R,14R,15R,16S)-5,16-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecan-14-yl]pentanamido]acetic acid

CAS Registry Number

360-65-6

SMILES

[H][C@]12CCC3C4CC[C@H]([C@H](C)CCC(=O)NCC(O)=O)[C@@]4(C)[C@@H](O)CC3[C@@]1(C)CC[C@@H](O)C2

InChI Identifier

InChI=1S/C26H43NO5/c1-15(4-9-23(30)27-14-24(31)32)19-7-8-20-18-6-5-16-12-17(28)10-11-25(16,2)21(18)13-22(29)26(19,20)3/h15-22,28-29H,4-14H2,1-3H3,(H,27,30)(H,31,32)/t15-,16-,17-,18?,19-,20?,21?,22+,25+,26-/m1/s1

InChI Key

WVULKSPCQVQLCU-ZMBDPXIHSA-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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Glycinated bile acids and derivatives

Alternative Parents

Substituents

Glycinated bile acid
Dihydroxy bile acid, alcohol, or derivatives
Hydroxy bile acid, alcohol, or derivatives
3-hydroxysteroid
12-hydroxysteroid
Hydroxysteroid
3-alpha-hydroxysteroid
N-acyl-alpha-amino acid
N-acyl-alpha amino acid or derivatives
Alpha-amino acid or derivatives
Fatty amide
Fatty acyl
N-acyl-amine
Cyclic alcohol
Carboxamide group
Secondary alcohol
Secondary carboxylic acid amide
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Hydrocarbon derivative
Organic oxide
Alcohol
Organic nitrogen compound
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organooxygen compound
Organonitrogen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Ontology

Disposition

Route of exposure:

Enteral:

Ingestion

Extracellular

Tissue and substructures:

Hepatic tissue

Subcellular:

Biofluid and excreta:

Organ and components:

Prostate

Process

Naturally occurring process:

Biological process:

Biochemical process:

Chemical reaction:

Lipid peroxidation

Cellular process:

Cell signaling

Biochemical pathway:

Role

Industrial application:

Biological role:

Molecular messenger:

Signaling molecule

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.0027 mg/mL	Not Available
LogP	2.25	RODA,A ET AL. (1990)

Predicted Properties

Property	Value	Source
Water Solubility	0.0078 g/L	ALOGPS
logP	2.69	ALOGPS
logP	2.69	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	3.77	ChemAxon
pKa (Strongest Basic)	-0.32	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	106.86 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	122 m³·mol⁻¹	ChemAxon
Polarizability	52.11 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-001i-0124900000-9935025b691abf76f837	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0udj-2101139000-a160ba76c005cfc50ac7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0ik9-0000900000-4a3e850d7237d0106c35	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-01ti-3894300000-fa0e7861362d7bf348bb	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0a7i-5910000000-17134bf01487bc71d373	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0gz9-2002900000-02545f99732b7619c59d	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-056r-9005400000-282d54d2414239340bc6	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-9104100000-4eb16c3c40c7f98e3788	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0000900000-9e4d382267acd7d0da8c	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00ea-4103900000-d0ad37cdb8c4ebcc8b3f	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-05fr-9001000000-23d56965528e66b241e7	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Extracellular

Biospecimen Locations

Bile
Blood
Feces
Urine

Tissue Locations

Prostate

Pathways

Name	SMPDB/Pathwhiz	KEGG
Bile Acid Biosynthesis
Congenital Bile Acid Synthesis Defect Type II		Not Available
Congenital Bile Acid Synthesis Defect Type III		Not Available
Familial Hypercholanemia (FHCA)		Not Available
Zellweger Syndrome		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Bile	Detected and Quantified	>0.01 uM	Adult (>18 years old)	Both	Normal	659989	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	20143319	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	29808030	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	27543620	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Normal	25037050	details
Feces	Detected and Quantified	19.19 +/- 13.69 nmol/g dry feces	Not Specified	Not Specified	Normal	22664055	details

Abnormal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Pancreatic ductal adenocarcinoma	20143319	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Hepatocellular carcinoma	22882828	details
Blood	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Liver Cirrhosis	22882828	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal Cancer	27275383	details
Feces	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Both	Colorectal cancer	25037050	details
Urine	Detected but not Quantified	Not Quantified	Adult (>18 years old)	Female	Epithelial ovarian cancer	23163809	details

Associated Disorders and Diseases

Disease References

Hepatocellular carcinoma
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
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 ]
Colorectal cancer
Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ] Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]

Associated OMIM IDs

114550 (Hepatocellular carcinoma)
114500 (Colorectal cancer)

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022152

KNApSAcK ID

Not Available

Chemspider ID

17215983

KEGG Compound ID

C05464

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5604

PubChem Compound

22833539

PDB ID

Not Available

ChEBI ID

27471

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

References

Synthesis Reference

Parmentier G; Eyssen H Synthesis and characteristics of the specific monosulfates of chenodeoxycholate, deoxycholate and their taurine or glycine conjugates. Steroids (1977), 30(5), 583-90.

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Bloch CA, Watkins JB: Determination of conjugated bile acids in human bile and duodenal fluid by reverse-phase high-performance liquid chromatography. J Lipid Res. 1978 May;19(4):510-3. [PubMed:659989 ]
Demers LM, Hepner GW: Levels of immunoreactive glycine-conjugated bile acids in health and hepatobiliary disease. Am J Clin Pathol. 1976 Nov;66(5):831-9. [PubMed:983991 ]
Demers LM, Hepner G: Radioimmunoassay of bile acids in serum. Clin Chem. 1976 May;22(5):602-6. [PubMed:1261008 ]
Hepner GW, Demers LM: Dynamics of the enterohepatic circulation of the glycine conjugates of cholic, chenodeoxycholic, deoxycholic, and sulfolithocholic acid in man. Gastroenterology. 1977 Mar;72(3):499-501. [PubMed:832799 ]
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. doi: 10.1038/nature07762. [PubMed:19212411 ]
Goto T, Myint KT, Sato K, Wada O, Kakiyama G, Iida T, Hishinuma T, Mano N, Goto J: LC/ESI-tandem mass spectrometric determination of bile acid 3-sulfates in human urine 3beta-Sulfooxy-12alpha-hydroxy-5beta-cholanoic acid is an abundant nonamidated sulfate. J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Feb 1;846(1-2):69-77. Epub 2006 Sep 1. [PubMed:16949895 ]

Enzymes

Enzyme Details

1. Glycine N-acyltransferase

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Mitochondrial acyltransferase which transfers an acyl group to the N-terminus of glycine and glutamine, although much less efficiently. Can conjugate numerous substrates to form a variety of N-acylglycines, with a preference for benzoyl-CoA over phenylacetyl-CoA as acyl donors. Thereby detoxify xenobiotics, such as benzoic acid or salicylic acid, and endogenous organic acids, such as isovaleric acid.
Gene Name:: GLYAT
Uniprot ID:: Q6IB77
Molecular weight:: 18506.33

Enzyme Details

2. Glycine N-acyltransferase-like protein 1

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Acyltransferase which transfers an acyl group to the N-terminus of glutamine. Can use phenylacetyl-CoA as an acyl donor.
Gene Name:: GLYATL1
Uniprot ID:: Q969I3
Molecular weight:: 35100.895

Enzyme Details

3. Glycine N-acyltransferase-like protein 2

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Mitochondrial acyltransferase which transfers the acyl group to the N-terminus of glycine. Conjugates numerous substrates, such as arachidonoyl-CoA and saturated medium and long-chain acyl-CoAs ranging from chain-length C8:0-CoA to C18:0-CoA, to form a variety of N-acylglycines. Shows a preference for monounsaturated fatty acid oleoyl-CoA (C18:1-CoA) as an acyl donor. Does not exhibit any activity toward C22:6-CoA and chenodeoxycholoyl-CoA, nor toward serine or alanine.
Gene Name:: GLYATL2
Uniprot ID:: Q8WU03
Molecular weight:: 34277.055

Enzyme Details

4. Glycine N-acyltransferase-like protein 3

General function:: Involved in glycine N-acyltransferase activity
Specific function:: Acyltransferase which transfers the acyl group to the N- terminus of glycine
Gene Name:: GLYATL3
Uniprot ID:: Q5SZD4
Molecular weight:: 32703.3

Showing metabocard for Deoxycholic acid glycine conjugate (HMDB0000631)

Structure for HMDB0000631 (Deoxycholic acid glycine conjugate)

Enzymes