NP-MRD: Showing NP-Card for (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid (NP0177285)

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Record Information

Version

2.0

Created at

2022-09-03 15:05:59 UTC

Updated at

2022-09-03 15:05:59 UTC

NP-MRD ID

NP0177285

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid

Description

Pinicolic acid B, also known as pinicolate b, belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid is found in Fomitopsis pinicola. (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid was first documented in 2020 (PMID: 31855822). Based on a literature review very few articles have been published on Pinicolic acid B.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032217062D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309032217062D          

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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  7  6  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
 11  7  1  6  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  1  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 11 21  1  0  0  0  0
 15 21  1  0  0  0  0
 21 22  1  6  0  0  0
 18 23  1  0  0  0  0
 23 24  1  6  0  0  0
 23 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  2  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
 29 32  1  0  0  0  0
 23 32  1  0  0  0  0
 32 33  1  6  0  0  0
 33 34  1  0  0  0  0
 17 34  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0177285

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@H]([C@H]1C(=O)C[C@@]2(C)C3=C(CC[C@]12C)[C@@]1(C)CCC(=O)C(C)(C)[C@@H]1CC3)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C30H44O4/c1-18(2)9-8-10-19(26(33)34)25-22(31)17-30(7)21-11-12-23-27(3,4)24(32)14-15-28(23,5)20(21)13-16-29(25,30)6/h9,19,23,25H,8,10-17H2,1-7H3,(H,33,34)/t19-,23+,25+,28-,29-,30+/m1/s1

> <INCHI_KEY>
RWQINIOQZXZDGZ-JLPRQSABSA-N

> <FORMULA>
C30H44O4

> <MOLECULAR_WEIGHT>
468.678

> <EXACT_MASS>
468.323959897

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
54.986563759162564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-6-methyl-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5,13-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]hept-5-enoic acid

> <JCHEM_LOGP>
6.282675100333335

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.68921270370172

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.677989873824409

> <JCHEM_PKA_STRONGEST_BASIC>
-7.160998155640733

> <JCHEM_POLAR_SURFACE_AREA>
71.44

> <JCHEM_REFRACTIVITY>
136.081

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-6-methyl-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5,13-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]hept-5-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0      16.349  -3.280   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.823  -3.490   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.243  -4.917   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.878  -2.275   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      12.353  -2.485   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      11.407  -1.269   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.882  -1.480   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.302  -2.907   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      10.247  -4.122   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       7.776  -3.117   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.937  -0.264   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.365   1.215   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      10.813   1.738   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       8.090   2.079   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       6.874   1.134   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       6.505   2.629   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.358   1.405   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.366   0.228   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.889  -1.221   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.405  -1.492   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       7.398  -0.314   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       8.069  -1.700   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.850   0.499   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       3.373  -0.949   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       1.857  -0.678   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.341  -0.407   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.182   1.041   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.698   1.312   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.810   2.218   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -0.521   2.992   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       1.341   3.664   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       2.326   1.947   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.319   3.125   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       4.835   2.854   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   11                                                  
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    7   12   21                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17   21                                             
CONECT   16   15                                                            
CONECT   17   15   18   34                                                  
CONECT   18   17   19   23                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   11   15   22                                             
CONECT   22   21                                                            
CONECT   23   18   24   25   32                                             
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30   31   32                                             
CONECT   30   29                                                            
CONECT   31   29                                                            
CONECT   32   29   23   33                                                  
CONECT   33   32   34                                                       
CONECT   34   33   17                                                       
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Value	Source
Pinicolate b	Generator

Chemical Formula

C₃₀H₄₄O₄

Average Mass

468.6780 Da

Monoisotopic Mass

468.32396 Da

IUPAC Name

(2R)-6-methyl-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5,13-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]hept-5-enoic acid

Traditional Name

(2R)-6-methyl-2-[(2S,7R,11R,14R,15R)-2,6,6,11,15-pentamethyl-5,13-dioxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadec-1(10)-en-14-yl]hept-5-enoic acid

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@H]([C@H]1C(=O)C[C@@]2(C)C3=C(CC[C@]12C)[C@@]1(C)CCC(=O)C(C)(C)[C@@H]1CC3)C(O)=O

InChI Identifier

InChI=1S/C30H44O4/c1-18(2)9-8-10-19(26(33)34)25-22(31)17-30(7)21-11-12-23-27(3,4)24(32)14-15-28(23,5)20(21)13-16-29(25,30)6/h9,19,23,25H,8,10-17H2,1-7H3,(H,33,34)/t19-,23+,25+,28-,29-,30+/m1/s1

InChI Key

RWQINIOQZXZDGZ-JLPRQSABSA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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
Fomitopsis pinicola	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Bile acid, alcohol, or derivatives
Steroid acid
3-oxosteroid
14-alpha-methylsteroid
16-oxosteroid
Oxosteroid
3-oxo-5-alpha-steroid
Steroid
Medium-chain fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Ketone
Cyclic ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Organic oxide
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	6.28	ChemAxon
pKa (Strongest Acidic)	4.68	ChemAxon
pKa (Strongest Basic)	-7.2	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	71.44 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	136.08 m³·mol⁻¹	ChemAxon
Polarizability	54.99 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

10187854

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15894361

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Grienke U, Kaserer T, Kirchweger B, Lambrinidis G, Kandel RT, Foster PA, Schuster D, Mikros E, Rollinger JM: Steroid sulfatase inhibiting lanostane triterpenes - Structure activity relationship and in silico insights. Bioorg Chem. 2020 Jan;95:103495. doi: 10.1016/j.bioorg.2019.103495. Epub 2019 Dec 9. [PubMed:31855822 ]
LOTUS database [Link]

Showing NP-Card for (2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid (NP0177285)

MOL for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D MOL for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D SDF for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D-SDF for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

PDB for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D PDB for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

SMILES for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

INCHI for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

Structure for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D Structure for NP0177285 ((2r)-2-[(1r,3ar,5ar,9as,11ar)-3a,6,6,9a,11a-pentamethyl-2,7-dioxo-1h,3h,4h,5h,5ah,8h,9h,10h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)