NP-MRD: Showing NP-Card for (2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid (NP0209439)

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Record Information

Version

1.0

Created at

2022-09-05 06:51:00 UTC

Updated at

2022-09-05 06:51:00 UTC

NP-MRD ID

NP0209439

Secondary Accession Numbers

None

Natural Product Identification

Common Name

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

Description

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

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052208512D          

 34 37  0  0  1  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652309052208512D          

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  5  6  1  0  0  0  0
  7  6  1  6  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  1  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  6  0  0  0
 15 17  1  0  0  0  0
 17 18  2  0  0  0  0
 18 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  1  0  0  0  0
 24 25  1  1  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  1  0  0  0
 28 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  2  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 11 33  1  0  0  0  0
 15 33  1  0  0  0  0
 33 34  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0209439

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@H]([C@H]1C(=O)C[C@@]2(C)C3=CC[C@H]4C(C)(C)[C@@H](O)CC[C@]4(C)C3=CC[C@]12C)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/h9,11,13,19,23-25,32H,8,10,12,14-17H2,1-7H3,(H,33,34)/t19-,23+,24+,25+,28-,29-,30+/m1/s1

> <INCHI_KEY>
ZILGTWWGYWOZLX-YJAYWBJASA-N

> <FORMULA>
C30H44O4

> <MOLECULAR_WEIGHT>
468.678

> <EXACT_MASS>
468.323959897

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
78

> <JCHEM_AVERAGE_POLARIZABILITY>
55.29022355232998

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(2S,5S,7R,11R,14R,15R)-5-hydroxy-2,6,6,11,15-pentamethyl-13-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),9-dien-14-yl]-6-methylhept-5-enoic acid

> <JCHEM_LOGP>
5.357225738

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.618794118232604

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.652873135365246

> <JCHEM_PKA_STRONGEST_BASIC>
-0.7785409691821731

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
138.0199

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-[(2S,5S,7R,11R,14R,15R)-5-hydroxy-2,6,6,11,15-pentamethyl-13-oxotetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadeca-1(17),9-dien-14-yl]-6-methylhept-5-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-SEP-22         0                                  
HETATM    1  C   UNK     0      -1.320  -5.020   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.206  -5.231   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.151  -4.015   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.786  -6.657   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.312  -6.868   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.257  -5.652   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.782  -5.863   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.363  -7.289   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       6.888  -7.500   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.417  -8.505   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.727  -4.647   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.299  -3.168   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       3.851  -2.645   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0       6.574  -2.304   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.790  -3.249   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.159  -1.754   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.306  -2.978   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.829  -1.529   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      11.345  -1.258   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      12.338  -2.436   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      13.854  -2.164   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      13.323  -0.719   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      15.185  -1.391   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.846  -3.342   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      16.362  -3.071   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0      14.323  -4.790   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      12.807  -5.061   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.814  -3.884   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      11.291  -5.332   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      10.299  -4.155   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       9.775  -5.603   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       8.259  -5.874   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       7.267  -4.697   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       6.595  -6.083   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   33                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   17   33                                             
CONECT   16   15                                                            
CONECT   17   15   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   20   29   30                                             
CONECT   29   28                                                            
CONECT   30   28   17   31                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   11   15   34                                             
CONECT   34   33                                                            
MASTER        0    0    0    0    0    0    0    0   34    0   74    0
END

View in JSmol

Synonyms

Value	Source
Pinicolate D	Generator

Chemical Formula

C₃₀H₄₄O₄

Average Mass

468.6780 Da

Monoisotopic Mass

468.32396 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@H]([C@H]1C(=O)C[C@@]2(C)C3=CC[C@H]4C(C)(C)[C@@H](O)CC[C@]4(C)C3=CC[C@]12C)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/h9,11,13,19,23-25,32H,8,10,12,14-17H2,1-7H3,(H,33,34)/t19-,23+,24+,25+,28-,29-,30+/m1/s1

InChI Key

ZILGTWWGYWOZLX-YJAYWBJASA-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
Cholesterol-skeleton
Cholestane-skeleton
Hydroxy bile acid, alcohol, or derivatives
Monohydroxy bile acid, alcohol, or derivatives
Bile acid, alcohol, or derivatives
Steroid acid
3-hydroxy-delta-7-steroid
3-hydroxysteroid
14-alpha-methylsteroid
Hydroxysteroid
16-oxosteroid
Oxosteroid
3-beta-hydroxysteroid
Steroid
Delta-7-steroid
Medium-chain fatty acid
Hydroxy fatty acid
Fatty acid
Unsaturated fatty acid
Fatty acyl
Cyclic alcohol
Cyclic ketone
Secondary alcohol
Ketone
Carboxylic acid
Carboxylic acid derivative
Monocarboxylic acid or derivatives
Organooxygen compound
Alcohol
Organic oxygen compound
Organic oxide
Carbonyl group
Hydrocarbon derivative
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

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

10187856

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

15894363

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,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid (NP0209439)

MOL for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D MOL for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D SDF for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D-SDF for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

PDB for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D PDB for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

SMILES for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

INCHI for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

Structure for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)

3D Structure for NP0209439 ((2r)-2-[(1r,3ar,5ar,7s,9as,11ar)-7-hydroxy-3a,6,6,9a,11a-pentamethyl-2-oxo-1h,3h,5h,5ah,7h,8h,9h,11h-cyclopenta[a]phenanthren-1-yl]-6-methylhept-5-enoic acid)