NP-MRD: Showing NP-Card for Chenodeoxyglycocholic acid (NP0087675)

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Record Information

Version

2.0

Created at

2022-05-11 16:56:33 UTC

Updated at

2022-05-11 16:56:34 UTC

NP-MRD ID

NP0087675

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Chenodeoxyglycocholic acid

Description

Chenodeoxyglycocholic acid 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. Chenodeoxyglycocholic acid is an extremely weak basic (essentially neutral) compound (based on its pKa). Bile acids recirculate through the liver, bile ducts, small intestine and portal vein to form an enterohepatic circuit. Bile acids are steroid acids found predominantly in bile of mammals. The unique detergent properties of bile acids are essential for the digestion and intestinal absorption of hydrophobic nutrients. Bile acids are physiological detergents that facilitate excretion, absorption, and transport of fats and sterols in the intestine and liver. They modulate bile flow and lipid secretion, are essential for the absorption of dietary fats and vitamins, and have been implicated in the regulation of all the key enzymes involved in cholesterol homeostasis.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv0541 02231220552D          

 32 35  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv0541 02231220552D          

 32 35  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
NP0087675

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(CCC(=O)NCC(O)=O)C1CCC2C3[C@H](O)CC4C[C@H](O)CC[C@]4(C)C3CC[C@]12C

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

> <INCHI_KEY>
GHCZAUBVMUEKKP-AFQLCFGXSA-N

> <FORMULA>
C26H43NO5

> <MOLECULAR_WEIGHT>
449.6233

> <EXACT_MASS>
449.314123491

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
51.805215356559074

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-{4-[(2S,5R,9R,15R)-5,9-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido}acetic acid

> <ALOGPS_LOGP>
2.40

> <JCHEM_LOGP>
2.608022284

> <ALOGPS_LOGS>
-4.75

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
15.791653018199973

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.773307537576899

> <JCHEM_PKA_STRONGEST_BASIC>
-0.2921848801328769

> <JCHEM_POLAR_SURFACE_AREA>
106.86000000000001

> <JCHEM_REFRACTIVITY>
122.07729999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.93e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
{4-[(2S,5R,9R,15R)-5,9-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido}acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

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      33.333 -22.706   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      25.885 -25.737   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      30.155 -23.451   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      30.796 -21.882   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      32.256 -25.737   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      31.350 -26.983   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      29.289 -22.202   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      23.217 -27.277   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      27.218 -24.967   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      24.551 -26.507   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      28.552 -24.197   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      24.551 -29.587   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      27.218 -29.587   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      26.277 -22.843   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      31.826 -23.026   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      25.885 -28.817   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      23.217 -28.817   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      31.350 -24.491   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      29.886 -26.507   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      27.218 -26.507   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      28.552 -28.817   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      28.259 -21.058   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      24.770 -23.163   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      28.552 -27.277   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      25.885 -27.277   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      29.886 -24.967   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      26.753 -21.378   0.000  0.00  0.00           N+0
HETATM   28  O   UNK     0      21.884 -29.587   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      29.886 -29.587   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      28.735 -19.593   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      23.740 -22.018   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      24.294 -24.627   0.000  0.00  0.00           O+0
CONECT    1   15                                                            
CONECT    2   25                                                            
CONECT    3   26                                                            
CONECT    4   15    7                                                       
CONECT    5   18    6                                                       
CONECT    6    5   19                                                       
CONECT    7    4   22                                                       
CONECT    8   10   17                                                       
CONECT    9   20   11                                                       
CONECT   10    8   25                                                       
CONECT   11    9   26                                                       
CONECT   12   17   16                                                       
CONECT   13   16   21                                                       
CONECT   14   27   23                                                       
CONECT   15    1    4   18                                                  
CONECT   16   12   13   25                                                  
CONECT   17    8   12   28                                                  
CONECT   18    5   15   26                                                  
CONECT   19    6   24   26                                                  
CONECT   20    9   24   25                                                  
CONECT   21   13   24   29                                                  
CONECT   22    7   30   27                                                  
CONECT   23   14   31   32                                                  
CONECT   24   19   20   21                                                  
CONECT   25    2   10   16   20                                             
CONECT   26    3   11   18   19                                             
CONECT   27   14   22                                                       
CONECT   28   17                                                            
CONECT   29   21                                                            
CONECT   30   22                                                            
CONECT   31   23                                                            
CONECT   32   23                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

View in JSmol

Synonyms

Value	Source
Chenodeoxyglycocholate	Generator
2-({4-[(2S,5R,9R,15R)-5,9-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]-1-hydroxypentylidene}amino)acetate	Generator

Chemical Formula

C₂₆H₄₃NO₅

Average Mass

449.6233 Da

Monoisotopic Mass

449.31412 Da

IUPAC Name

2-{4-[(2S,5R,9R,15R)-5,9-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido}acetic acid

Traditional Name

{4-[(2S,5R,9R,15R)-5,9-dihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanamido}acetic acid

CAS Registry Number

Not Available

SMILES

CC(CCC(=O)NCC(O)=O)C1CCC2C3[C@H](O)CC4C[C@H](O)CC[C@]4(C)C3CC[C@]12C

InChI Identifier

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

InChI Key

GHCZAUBVMUEKKP-AFQLCFGXSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Anas platyrhynchos	FooDB	FooDB
Anatidae	FooDB	FooDB
Anser anser	FooDB	FooDB
Bison bison	FooDB	FooDB
Bos taurus	FooDB	FooDB
Bos taurus X Bison bison	FooDB	FooDB
Bubalus bubalis	FooDB	FooDB
Capra aegagrus hircus	FooDB	FooDB
Cervidae	FooDB	FooDB
Cervus canadensis	FooDB	FooDB
Columba	FooDB	FooDB
Columbidae	FooDB	FooDB
Dromaius novaehollandiae	FooDB	FooDB
Equus caballus	FooDB	FooDB
Gallus gallus	FooDB	FooDB
Lagopus muta	FooDB	FooDB
Leporidae	FooDB	FooDB
Lepus timidus	FooDB	FooDB
Melanitta fusca	FooDB	FooDB
Meleagris gallopavo	FooDB	FooDB
Numida meleagris	FooDB	FooDB
Odocoileus	FooDB	FooDB
Oryctolagus	FooDB	FooDB
Ovis aries	FooDB	FooDB
Phasianidae	FooDB	FooDB
Phasianus colchicus	FooDB	FooDB
Struthio camelus	FooDB	FooDB
Sus scrofa	FooDB	FooDB
Sus scrofa domestica	FooDB	FooDB

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
Hydroxysteroid
7-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
Secondary carboxylic acid amide
Secondary alcohol
Carboxamide group
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Organooxygen compound
Organopnictogen compound
Organic nitrogen compound
Organic oxide
Hydrocarbon derivative
Alcohol
Carbonyl group
Organic oxygen compound
Organonitrogen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	2.4	ALOGPS
logP	2.61	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	3.77	ChemAxon
pKa (Strongest Basic)	-0.29	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	122.08 m³·mol⁻¹	ChemAxon
Polarizability	51.81 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

External Links

HMDB ID

HMDB0006898

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB024145

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

C05462

BioCyc ID

Not Available

BiGG ID

45858

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

53477907

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Chenodeoxyglycocholic acid (NP0087675)

MOL for NP0087675 (Chenodeoxyglycocholic acid)

3D MOL for NP0087675 (Chenodeoxyglycocholic acid)

3D SDF for NP0087675 (Chenodeoxyglycocholic acid)

3D-SDF for NP0087675 (Chenodeoxyglycocholic acid)

PDB for NP0087675 (Chenodeoxyglycocholic acid)

3D PDB for NP0087675 (Chenodeoxyglycocholic acid)

SMILES for NP0087675 (Chenodeoxyglycocholic acid)

INCHI for NP0087675 (Chenodeoxyglycocholic acid)

Structure for NP0087675 (Chenodeoxyglycocholic acid)

3D Structure for NP0087675 (Chenodeoxyglycocholic acid)