NP-MRD: Showing NP-Card for 1,3,12-Trihydroxycholan-24-oic acid (NP0086563)

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Record Information

Version

2.0

Created at

2022-05-11 16:24:32 UTC

Updated at

2022-05-11 16:24:32 UTC

NP-MRD ID

NP0086563

Secondary Accession Numbers

None

Natural Product Identification

Common Name

1,3,12-Trihydroxycholan-24-oic acid

Description

PG(18:0/20:3(8Z,11Z,14Z)) is a phosphatidylglycerol. Phosphatidylglycerols consist of a glycerol 3-phosphate backbone esterified to either saturated or unsaturated fatty acids on carbons 1 and 2. As is the case with diacylglycerols, phosphatidylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions. PG(18:0/20:3(8Z,11Z,14Z)), in particular, consists of one octadecanoyl chain to the C-1 atom, and one 8Z,11Z,14Z-eicosatrienoyl to the C-2 atom. In E. Coli glycerophospholipid metabolism, phosphatidylglycerol is formed from phosphatidic acid (1,2-diacyl-sn-glycerol 3-phosphate) by a sequence of enzymatic reactions that proceeds via two intermediates, cytidine diphosphate diacylglycerol (CDP-diacylglycerol) and phosphatidylglycerophosphate (PGP, a phosphorylated phosphatidylglycerol). Phosphatidylglycerols, along with CDP-diacylglycerol, also serve as precursor molecules for the synthesis of cardiolipin, a phospholipid found in membranes.

Structure

MOL 3D MOL SDF PDB SMILES InChI

Untitled Document-5
  Mrv0541 02231218292D          

 32 35  0  0  0  0            999 V2000
   -3.1748   -1.4821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1748   -2.3071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4604   -2.7196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7459   -2.3071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7459   -1.4821    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.4604   -1.0696    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0314   -2.7196    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3170   -2.3071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3170   -1.4821    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0314   -1.0696    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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    0.3975   -0.2446    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3170    0.1679    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.6671   -0.6571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  2 18  1  0  0  0  0
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  9 21  1  1  0  0  0
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 11 30  1  6  0  0  0
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 23 32  1  6  0  0  0
M  END

     RDKit          3D

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    3.3893   -1.5999    0.4621 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.1386   -2.2936    1.6524 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7599   -0.2191    0.4666 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.3986    0.1182    1.8819 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5718   -0.2189   -0.4833 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.6390   -1.3389   -0.2488 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7697   -1.0322    0.0562 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -1.2996    0.2699   -0.3480 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.7445    1.1341    0.8016 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.8598    1.6162    0.4827 H   0  0  0  0  0  0  0  0  0  0  0  0
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  3  4  1  0
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 23 61  1  0
M  END

Untitled Document-5
  Mrv0541 02231218292D          

 32 35  0  0  0  0            999 V2000
   -3.1748   -1.4821    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1748   -2.3071    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 23 32  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0086563

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@H]([C@H](C)CCC(O)=O)[C@@]1(C)C(O)C[C@@]1([H])[C@@]2([H])CCC2CC(O)CC(O)[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C24H40O5/c1-13(4-9-22(28)29)17-7-8-18-16-6-5-14-10-15(25)11-20(26)23(14,2)19(16)12-21(27)24(17,18)3/h13-21,25-27H,4-12H2,1-3H3,(H,28,29)/t13-,14?,15?,16+,17-,18+,19+,20?,21?,23+,24-/m1/s1

> <INCHI_KEY>
DAKYVYUAVGJDRK-JZBKOBKOSA-N

> <FORMULA>
C24H40O5

> <MOLECULAR_WEIGHT>
408.5714

> <EXACT_MASS>
408.28757439

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
47.45691781914301

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(4R)-4-[(1S,2S,10S,11S,14R,15R)-3,5,16-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

> <ALOGPS_LOGP>
2.46

> <JCHEM_LOGP>
2.4876541806666665

> <ALOGPS_LOGS>
-3.74

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.504114691409988

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.651656368792817

> <JCHEM_PKA_STRONGEST_BASIC>
-0.3963359038911446

> <JCHEM_POLAR_SURFACE_AREA>
97.99

> <JCHEM_REFRACTIVITY>
110.66869999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.35e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-4-[(1S,2S,10S,11S,14R,15R)-3,5,16-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Untitled Document-5                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -5.926  -2.767   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.926  -4.307   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.593  -5.077   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.259  -4.307   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -3.259  -2.767   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -4.593  -1.997   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.925  -5.077   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -0.592  -4.307   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -0.592  -2.767   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.925  -1.997   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.742  -1.997   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.742  -0.457   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.592   0.313   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -1.925  -0.457   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.207  -2.472   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.112  -1.227   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.207   0.019   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      -7.260  -5.077   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      -4.593  -0.457   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      -3.259  -1.227   0.000  0.00  0.00           C+0
HETATM   21  H   UNK     0       0.497  -3.855   0.000  0.00  0.00           H+0
HETATM   22  C   UNK     0       0.903   1.075   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.683   1.484   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       4.189   1.804   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       4.665   3.269   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       6.171   3.589   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       6.570   5.077   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       7.260   2.500   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0      -0.592   1.853   0.000  0.00  0.00           O+0
HETATM   30  H   UNK     0       1.512  -3.330   0.000  0.00  0.00           H+0
HETATM   31  H   UNK     0      -0.592  -1.227   0.000  0.00  0.00           H+0
HETATM   32  C   UNK     0       1.594   2.573   0.000  0.00  0.00           C+0
CONECT    1    2    6                                                       
CONECT    2    1    3   18                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    7                                                  
CONECT    5    4    6   10   20                                             
CONECT    6    5    1   19                                                  
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   21                                             
CONECT   10    9    5   14   31                                             
CONECT   11    9   12   15   30                                             
CONECT   12   11   13   17   22                                             
CONECT   13   12   14   29                                                  
CONECT   14   13   10                                                       
CONECT   15   11   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12   23                                                  
CONECT   18    2                                                            
CONECT   19    6                                                            
CONECT   20    5                                                            
CONECT   21    9                                                            
CONECT   22   12                                                            
CONECT   23   17   24   32                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   13                                                            
CONECT   30   11                                                            
CONECT   31   10                                                            
CONECT   32   23                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   70    0
END

View in JSmol

Synonyms

Value	Source
1,3,12-Trihydroxy-5b-cholanoate	HMDB
1,3,12-Trihydroxy-5b-cholanoic acid	HMDB
1,3,12-Trihydroxy-cholan-24-Oate	HMDB
1,3,12-Trihydroxy-cholan-24-Oic acid	HMDB
1,3,12-Trihydroxycholan-24-Oate	HMDB, Generator
1 beta,3 alpha,12 alpha-Trihydroxy-5 beta-cholanoic acid	MeSH, HMDB
1,3,12-Trihydroxycholanoic acid	MeSH, HMDB
(4R)-4-[(1S,2S,10S,11S,14R,15R)-3,5,16-Trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoate	Generator, HMDB

Chemical Formula

C₂₄H₄₀O₅

Average Mass

408.5714 Da

Monoisotopic Mass

408.28757 Da

IUPAC Name

(4R)-4-[(1S,2S,10S,11S,14R,15R)-3,5,16-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

Traditional Name

(4R)-4-[(1S,2S,10S,11S,14R,15R)-3,5,16-trihydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]pentanoic acid

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@H]([C@H](C)CCC(O)=O)[C@@]1(C)C(O)C[C@@]1([H])[C@@]2([H])CCC2CC(O)CC(O)[C@]12C

InChI Identifier

InChI=1S/C24H40O5/c1-13(4-9-22(28)29)17-7-8-18-16-6-5-14-10-15(25)11-20(26)23(14,2)19(16)12-21(27)24(17,18)3/h13-21,25-27H,4-12H2,1-3H3,(H,28,29)/t13-,14?,15?,16+,17-,18+,19+,20?,21?,23+,24-/m1/s1

InChI Key

DAKYVYUAVGJDRK-JZBKOBKOSA-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 phosphatidylglycerols. These are glycerophosphoglycerols in which two fatty acids are bonded to the 1-glycerol moiety through ester linkages. As is the case with diacylglycerols, phosphatidylglycerols can have many different combinations of fatty acids of varying lengths and saturation attached to the C-1 and C-2 positions.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Glycerophospholipids

Sub Class

Glycerophosphoglycerols

Direct Parent

Phosphatidylglycerols

Alternative Parents

Substituents

1,2-diacylglycerophosphoglycerol
Fatty acid ester
Dialkyl phosphate
Dicarboxylic acid or derivatives
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Fatty acyl
1,2-diol
Carboxylic acid ester
Secondary alcohol
Carboxylic acid derivative
Organic oxide
Organooxygen compound
Alcohol
Organic oxygen compound
Primary alcohol
Carbonyl group
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic 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	2.46	ALOGPS
logP	2.49	ChemAxon
logS	-3.7	ALOGPS
pKa (Strongest Acidic)	4.65	ChemAxon
pKa (Strongest Basic)	-0.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	110.67 m³·mol⁻¹	ChemAxon
Polarizability	47.46 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB027759

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Not Available

Showing NP-Card for 1,3,12-Trihydroxycholan-24-oic acid (NP0086563)

MOL for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

3D MOL for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

3D SDF for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

3D-SDF for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

PDB for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

3D PDB for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

SMILES for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

INCHI for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

Structure for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)

3D Structure for NP0086563 (1,3,12-Trihydroxycholan-24-oic acid)