NP-MRD: Showing NP-Card for Varanic acid (NP0086903)

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Record Information

Version

2.0

Created at

2022-05-11 16:34:13 UTC

Updated at

2022-05-11 16:34:14 UTC

NP-MRD ID

NP0086903

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Varanic acid

Description

Varanic acid, also known as varanate, belongs to the class of organic compounds known as trihydroxy bile acids, alcohols and derivatives. These are prenol lipids structurally characterized by a bile acid or alcohol which bears three hydroxyl groups. Varanic acid was first documented in 1989 (PMID: 2706931). Varanic acid is an extremely weak basic (essentially neutral) compound (based on its pKa) (PMID: 9831634) (PMID: 2318981).

Structure

MOL 3D MOL SDF PDB SMILES InChI

Untitled Document-7
  Mrv0541 02231219252D          

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M  END

     RDKit          3D

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M  END

Untitled Document-7
  Mrv0541 02231219252D          

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 21 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 22 26  1  1  0  0  0
 12 27  1  1  0  0  0
  9 28  1  1  0  0  0
  5 29  1  1  0  0  0
  4 30  1  1  0  0  0
  2 31  1  6  0  0  0
 10 32  1  6  0  0  0
 11 33  1  6  0  0  0
 18 34  1  6  0  0  0
 21 35  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0086903

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C26H44O5/c1-15(4-9-22(28)23(29)24(30)31)19-7-8-20-18-6-5-16-14-17(27)10-12-25(16,2)21(18)11-13-26(19,20)3/h15-23,27-29H,4-14H2,1-3H3,(H,30,31)/t15-,16-,17-,18+,19-,20+,21+,22-,23-,25+,26-/m1/s1

> <INCHI_KEY>
NRDKNLGDNLHWHG-IYELHLJQSA-N

> <FORMULA>
C26H44O5

> <MOLECULAR_WEIGHT>
436.6246

> <EXACT_MASS>
436.318874518

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_AVERAGE_POLARIZABILITY>
51.20869193776398

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,6R)-2,3-dihydroxy-6-[(1S,2S,5R,7R,10R,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]heptanoic acid

> <ALOGPS_LOGP>
3.41

> <JCHEM_LOGP>
3.9652381229999993

> <ALOGPS_LOGS>
-4.73

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.263371978703038

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.048691821334989

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3569579557624003

> <JCHEM_POLAR_SURFACE_AREA>
97.99000000000001

> <JCHEM_REFRACTIVITY>
119.73699999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.10e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
varanic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Untitled Document-7                               
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0      -6.870  -3.325   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -6.870  -4.865   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -5.536  -5.635   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.202  -4.865   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.202  -3.325   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -5.536  -2.555   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.868  -5.635   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.535  -4.865   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -1.535  -3.325   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.868  -2.555   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -0.201  -2.555   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      -0.201  -1.015   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.535  -0.245   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.868  -1.015   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.264  -3.031   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.169  -1.785   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.264  -0.539   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.740   0.926   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.246   1.246   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.722   2.711   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       5.228   3.031   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.627   4.518   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       7.114   4.917   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       7.513   6.405   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       8.203   3.828   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       4.538   5.607   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.040   0.517   0.000  0.00  0.00           C+0
HETATM   28  H   UNK     0      -0.446  -4.414   0.000  0.00  0.00           H+0
HETATM   29  C   UNK     0      -4.972  -1.991   0.000  0.00  0.00           C+0
HETATM   30  H   UNK     0      -4.202  -6.405   0.000  0.00  0.00           H+0
HETATM   31  O   UNK     0      -8.203  -5.635   0.000  0.00  0.00           O+0
HETATM   32  H   UNK     0      -3.957  -1.466   0.000  0.00  0.00           H+0
HETATM   33  H   UNK     0       0.569  -3.888   0.000  0.00  0.00           H+0
HETATM   34  C   UNK     0       0.651   2.015   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       6.317   1.942   0.000  0.00  0.00           O+0
CONECT    1    2    6                                                       
CONECT    2    1    3   31                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    7   30                                             
CONECT    5    4    6   10   29                                             
CONECT    6    5    1                                                       
CONECT    7    4    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   28                                             
CONECT   10    9    5   14   32                                             
CONECT   11    9   12   15   33                                             
CONECT   12   11   13   17   27                                             
CONECT   13   12   14                                                       
CONECT   14   13   10                                                       
CONECT   15   11   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   12   18                                                  
CONECT   18   17   19   34                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   35                                                  
CONECT   22   21   23   26                                                  
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23                                                            
CONECT   26   22                                                            
CONECT   27   12                                                            
CONECT   28    9                                                            
CONECT   29    5                                                            
CONECT   30    4                                                            
CONECT   31    2                                                            
CONECT   32   10                                                            
CONECT   33   11                                                            
CONECT   34   18                                                            
CONECT   35   21                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
Varanate	Generator
3a,7a,12a,24-Tetrahydroxy-5b-cholestan-26-Oate	HMDB
3a,7a,12a,24-Tetrahydroxy-5b-cholestan-26-Oic acid	HMDB
3a,7a,12a,24-Tetrahydroxy-5b-cholestanoate	HMDB
3a,7a,12a,24-Tetrahydroxy-5b-cholestanoic acid	HMDB
3alpha,7alpha,12alpha, 24-Tetrahydroxy-5beta-cholest-26-Oate	HMDB
3alpha,7alpha,12alpha, 24-Tetrahydroxy-5beta-cholest-26-Oic acid	HMDB
Baranate	HMDB
Baranic acid	HMDB
(2R,3R,6R)-2,3-Dihydroxy-6-[(1S,2S,5R,7R,10R,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]heptanoate	HMDB

Chemical Formula

C₂₆H₄₄O₅

Average Mass

436.6246 Da

Monoisotopic Mass

436.31887 Da

IUPAC Name

(2R,3R,6R)-2,3-dihydroxy-6-[(1S,2S,5R,7R,10R,11S,14R,15R)-5-hydroxy-2,15-dimethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl]heptanoic acid

Traditional Name

varanic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C26H44O5/c1-15(4-9-22(28)23(29)24(30)31)19-7-8-20-18-6-5-16-14-17(27)10-12-25(16,2)21(18)11-13-26(19,20)3/h15-23,27-29H,4-14H2,1-3H3,(H,30,31)/t15-,16-,17-,18+,19-,20+,21+,22-,23-,25+,26-/m1/s1

InChI Key

NRDKNLGDNLHWHG-IYELHLJQSA-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 trihydroxy bile acids, alcohols and derivatives. These are prenol lipids structurally characterized by a bile acid or alcohol which bears three 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

Trihydroxy bile acids, alcohols and derivatives

Alternative Parents

Substituents

Cholesterol-skeleton
Cholestane-skeleton
25-hydroxysteroid
Trihydroxy bile acid, alcohol, or derivatives
24-hydroxysteroid
Steroid acid
3-hydroxysteroid
Hydroxysteroid
3-alpha-hydroxysteroid
Medium-chain hydroxy acid
Medium-chain fatty acid
Beta-hydroxy acid
Hydroxy fatty acid
Monosaccharide
Alpha-hydroxy acid
Fatty acid
Fatty acyl
Hydroxy acid
Cyclic alcohol
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Carboxylic acid
Organooxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
Organic oxygen compound
Alcohol
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	3.41	ALOGPS
logP	3.97	ChemAxon
logS	-4.7	ALOGPS
pKa (Strongest Acidic)	4.05	ChemAxon
pKa (Strongest Basic)	-1.4	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	6	ChemAxon
Refractivity	119.74 m³·mol⁻¹	ChemAxon
Polarizability	51.21 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

HMDB0002195

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

FDB022897

KNApSAcK ID

Not Available

Chemspider ID

17216172

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

6538

PubChem Compound

22833587

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Vreken P, van Rooij A, Denis S, van Grunsven EG, Cuebas DA, Wanders RJ: Sensitive analysis of serum 3alpha, 7alpha, 12alpha,24-tetrahydroxy- 5beta-cholestan-26-oic acid diastereomers using gas chromatography-mass spectrometry and its application in peroxisomal D-bifunctional protein deficiency. J Lipid Res. 1998 Dec;39(12):2452-8. [PubMed:9831634 ]
Casteels M, Schepers L, Parmentier G, Eyssen HJ, Mannaerts GP: Activation and peroxisomal beta-oxidation of fatty acids and bile acid intermediates in liver from Bombina orientalis and from the rat. Comp Biochem Physiol B. 1989;92(1):129-32. doi: 10.1016/0305-0491(89)90324-6. [PubMed:2706931 ]
Clayton PT, Patel E, Lawson AM, Carruthers RA, Collins J: Bile acid profiles in peroxisomal 3-oxoacyl-coenzyme A thiolase deficiency. J Clin Invest. 1990 Apr;85(4):1267-73. doi: 10.1172/JCI114563. [PubMed:2318981 ]

Showing NP-Card for Varanic acid (NP0086903)

MOL for NP0086903 (Varanic acid)

3D MOL for NP0086903 (Varanic acid)

3D SDF for NP0086903 (Varanic acid)

3D-SDF for NP0086903 (Varanic acid)

PDB for NP0086903 (Varanic acid)

3D PDB for NP0086903 (Varanic acid)

SMILES for NP0086903 (Varanic acid)

INCHI for NP0086903 (Varanic acid)

Structure for NP0086903 (Varanic acid)

3D Structure for NP0086903 (Varanic acid)