NP-MRD: Showing NP-Card for 5b-Cholestane-3a,7a,12a,24,25-pentol (NP0086612)

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Record Information

Version

2.0

Created at

2022-05-11 16:26:02 UTC

Updated at

2022-05-11 16:26:02 UTC

NP-MRD ID

NP0086612

Secondary Accession Numbers

None

Natural Product Identification

Common Name

5b-Cholestane-3a,7a,12a,24,25-pentol

Description

5B-Cholestane-3a,7a,12a,24,25-pentol, also known as 3a,7a,12a,24,25-pentahydroxycoprostane, belongs to the class of organic compounds known as pentahydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or derivatives bearing five hydroxyl groups. 5B-Cholestane-3a,7a,12a,24,25-pentol is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL 3D MOL SDF PDB SMILES InChI

5b-Cholestane-3a,7a,12a,24,25-pentol.mol
  Mrv1652305231918092D          

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M  END

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5b-Cholestane-3a,7a,12a,24,25-pentol.mol
  Mrv1652305231918092D          

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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  1  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 13 20  1  1  0  0  0
 12 21  1  0  0  0  0
  9 21  1  0  0  0  0
 21 22  1  1  0  0  0
 21 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
  8 25  1  0  0  0  0
 25 26  1  0  0  0  0
  3 26  1  0  0  0  0
  5 26  1  0  0  0  0
 26 27  1  1  0  0  0
 17 28  1  0  0  0  0
 16 29  1  0  0  0  0
 23 30  1  6  0  0  0
  7 31  1  6  0  0  0
  1 32  1  6  0  0  0
 25 33  1  6  0  0  0
  8 34  1  1  0  0  0
  9 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0086612

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]12CC[C@H]([C@H](C)CCC(O)C(C)(C)O)[C@@]1(C)[C@@H](O)C[C@@]1([H])[C@@]2([H])[C@H](O)CC2C[C@H](O)CC[C@]12C

> <INCHI_IDENTIFIER>
InChI=1S/C27H48O5/c1-15(6-9-22(30)25(2,3)32)18-7-8-19-24-20(14-23(31)27(18,19)5)26(4)11-10-17(28)12-16(26)13-21(24)29/h15-24,28-32H,6-14H2,1-5H3/t15-,16?,17-,18-,19+,20+,21-,22?,23+,24+,26+,27-/m1/s1

> <INCHI_KEY>
NHPWQASMMFUHIZ-OOOZRTEJSA-N

> <FORMULA>
C27H48O5

> <MOLECULAR_WEIGHT>
452.667

> <EXACT_MASS>
452.350174646

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
80

> <JCHEM_AVERAGE_POLARIZABILITY>
54.016796543418

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5R,9R,10R,11S,14R,15R,16S)-14-[(2R)-5,6-dihydroxy-6-methylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

> <ALOGPS_LOGP>
2.54

> <JCHEM_LOGP>
2.4328743559999992

> <ALOGPS_LOGS>
-4.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
15.325111730088558

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.849642772256644

> <JCHEM_PKA_STRONGEST_BASIC>
-0.15943471521408192

> <JCHEM_POLAR_SURFACE_AREA>
101.15

> <JCHEM_REFRACTIVITY>
126.0721

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.37e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5R,9R,10R,11S,14R,15R,16S)-14-[(2R)-5,6-dihydroxy-6-methylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 5b-Cholestane-3a,7a,12a,24,25-pentol.mol          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAY-19         0                                  
HETATM    1  C   UNK     0      -5.184  -5.386   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -5.184  -3.846   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -3.851  -3.076   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.851  -6.156   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.517  -5.386   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.183  -6.156   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.150  -5.386   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.150  -3.846   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.484  -3.076   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.949  -3.552   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.854  -2.306   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.949  -1.060   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.425   0.405   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.455   1.602   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.007   3.039   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.528   3.280   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.080   4.718   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       3.643   5.270   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.632   6.156   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.931   0.725   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.484  -1.536   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.484   0.004   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.150  -0.766   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -1.183  -1.536   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.183  -3.076   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -2.517  -3.846   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.517  -2.306   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0       6.518   4.166   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       5.498   2.083   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0       0.150   0.774   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       1.484  -6.156   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      -6.518  -6.156   0.000  0.00  0.00           O+0
HETATM   33  H   UNK     0      -1.183  -4.616   0.000  0.00  0.00           H+0
HETATM   34  H   UNK     0       0.150  -2.306   0.000  0.00  0.00           H+0
HETATM   35  H   UNK     0       1.484  -4.616   0.000  0.00  0.00           H+0
CONECT    1    2    4   32                                                  
CONECT    2    1    3                                                       
CONECT    3    2   26                                                       
CONECT    4    1    5                                                       
CONECT    5    4    6   26                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   31                                                  
CONECT    8    7    9   25   34                                             
CONECT    9    8   10   21   35                                             
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   21                                                  
CONECT   13   12   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   29                                                  
CONECT   17   16   18   19   28                                             
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   13                                                            
CONECT   21   12    9   22   23                                             
CONECT   22   21                                                            
CONECT   23   21   24   30                                                  
CONECT   24   23   25                                                       
CONECT   25   24    8   26   33                                             
CONECT   26   25    3    5   27                                             
CONECT   27   26                                                            
CONECT   28   17                                                            
CONECT   29   16                                                            
CONECT   30   23                                                            
CONECT   31    7                                                            
CONECT   32    1                                                            
CONECT   33   25                                                            
CONECT   34    8                                                            
CONECT   35    9                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
3a,7a,12a,24,25-Pentahydroxycoprostane	HMDB
3alpha,7alpha,12alpha,24R,25-Pentahydroxy-5beta-cholestane	HMDB
5beta-Cholestane-3alpha,7alpha,12alpha,24R,25-pentol	HMDB
5b-Cholestane-3a,7a,12a,24R,25-pentol	HMDB
5Β-cholestane-3α,7α,12α,24R,25-pentol	HMDB

Chemical Formula

C₂₇H₄₈O₅

Average Mass

452.6670 Da

Monoisotopic Mass

452.35017 Da

IUPAC Name

(1S,2S,5R,9R,10R,11S,14R,15R,16S)-14-[(2R)-5,6-dihydroxy-6-methylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

Traditional Name

(1S,2S,5R,9R,10R,11S,14R,15R,16S)-14-[(2R)-5,6-dihydroxy-6-methylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,9,16-triol

CAS Registry Number

Not Available

SMILES

[H][C@@]12CC[C@H]([C@H](C)CCC(O)C(C)(C)O)[C@@]1(C)[C@@H](O)C[C@@]1([H])[C@@]2([H])[C@H](O)CC2C[C@H](O)CC[C@]12C

InChI Identifier

InChI=1S/C27H48O5/c1-15(6-9-22(30)25(2,3)32)18-7-8-19-24-20(14-23(31)27(18,19)5)26(4)11-10-17(28)12-16(26)13-21(24)29/h15-24,28-32H,6-14H2,1-5H3/t15-,16?,17-,18-,19+,20+,21-,22?,23+,24+,26+,27-/m1/s1

InChI Key

NHPWQASMMFUHIZ-OOOZRTEJSA-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 pentahydroxy bile acids, alcohols and derivatives. These are bile acids, alcohols or derivatives bearing five hydroxyl groups.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Bile acids, alcohols and derivatives

Direct Parent

Pentahydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Pentahydroxy bile acid, alcohol, or derivatives
25-hydroxysteroid
24-hydroxysteroid
3-hydroxysteroid
12-hydroxysteroid
7-hydroxysteroid
3-alpha-hydroxysteroid
Hydroxysteroid
Cyclic alcohol
Tertiary alcohol
Secondary alcohol
Polyol
Alcohol
Hydrocarbon derivative
Organic oxygen compound
Organooxygen 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	2.54	ALOGPS
logP	2.43	ChemAxon
logS	-4	ALOGPS
pKa (Strongest Acidic)	13.85	ChemAxon
pKa (Strongest Basic)	-0.16	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	101.15 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	126.07 m³·mol⁻¹	ChemAxon
Polarizability	54.02 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	No	ChemAxon

External Links

HMDB ID

HMDB0000556

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022116

KNApSAcK ID

Not Available

Chemspider ID

13628107

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5540

PubChem Compound

21252253

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for 5b-Cholestane-3a,7a,12a,24,25-pentol (NP0086612)

MOL for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

3D MOL for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

3D SDF for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

3D-SDF for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

PDB for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

3D PDB for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

SMILES for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

INCHI for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

Structure for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)

3D Structure for NP0086612 (5b-Cholestane-3a,7a,12a,24,25-pentol)