NP-MRD: Showing NP-Card for (6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one (NP0213385)

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Record Information

Version

2.0

Created at

2022-09-05 12:21:38 UTC

Updated at

2022-09-05 12:21:38 UTC

NP-MRD ID

NP0213385

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one

Description

CHEMBL3581592 belongs to the class of organic compounds known as monocyclic monoterpenoids. These are monoterpenoids containing 1 ring in the isoprene chain. (6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one is found in Hypericum henryi. Based on a literature review very few articles have been published on CHEMBL3581592.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309052214212D          

 31 32  0  0  1  0            999 V2000
    1.4748   -3.9898    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1393   -3.2361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3188   -3.1499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6242   -2.5687    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4492   -2.5687    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7041   -1.7840    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0367   -1.2991    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.5887   -0.6860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4847   -0.6860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3693   -1.7840    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.5846   -1.5291    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4131   -0.7221    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3715   -0.4672    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9846   -1.0192    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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   -3.4814    1.2062   -0.1565 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652309052214212D          

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M  END
> <DATABASE_ID>
NP0213385

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)C(=O)C1=C(O)C(C[C@H]2[C@@H](CC[C@@]2(C)O)C(C)=C)=C(O)[C@@](C)(CC=C(C)C)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H38O5/c1-14(2)9-11-25(7)23(29)18(22(28)20(24(25)30)21(27)16(5)6)13-19-17(15(3)4)10-12-26(19,8)31/h9,16-17,19,28-29,31H,3,10-13H2,1-2,4-8H3/t17-,19-,25+,26+/m0/s1

> <INCHI_KEY>
QYPGFMLLGVPVHG-IPFQZCJUSA-N

> <FORMULA>
C26H38O5

> <MOLECULAR_WEIGHT>
430.585

> <EXACT_MASS>
430.271924324

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
69

> <JCHEM_AVERAGE_POLARIZABILITY>
47.756427347407126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(6R)-3,5-dihydroxy-4-{[(1S,2R,5R)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one

> <JCHEM_LOGP>
4.744641269666667

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.136491301471366

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.535198697267799

> <JCHEM_PKA_STRONGEST_BASIC>
-0.6701683802931403

> <JCHEM_POLAR_SURFACE_AREA>
94.83

> <JCHEM_REFRACTIVITY>
126.48459999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(6R)-3,5-dihydroxy-4-{[(1S,2R,5R)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one

> <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       2.753  -7.448   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.127  -6.041   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.595  -5.880   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.032  -4.795   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.572  -4.795   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.048  -3.330   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.802  -2.425   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.832  -1.281   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       2.771  -1.281   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       2.556  -3.330   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.091  -2.854   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.771  -1.348   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.693  -0.872   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -1.838  -1.903   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.014   0.634   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.442   0.057   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -1.830   1.940   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -3.369   1.887   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -4.185   3.193   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -5.724   3.139   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -3.462   4.552   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.131   1.665   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.189   3.171   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0       1.595   1.189   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.740   2.219   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0       4.204   1.743   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0       2.420   3.726   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       0.955   4.202   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.564   4.756   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.916  -0.317   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       3.380  -0.793   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7    4   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   30                                                  
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17   22                                             
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20   21                                                  
CONECT   20   19                                                            
CONECT   21   19                                                            
CONECT   22   15   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25   30                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27                                                            
CONECT   30   24   12   31                                                  
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   64    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₆H₃₈O₅

Average Mass

430.5850 Da

Monoisotopic Mass

430.27192 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC(C)C(=O)C1=C(O)C(C[C@H]2[C@@H](CC[C@@]2(C)O)C(C)=C)=C(O)[C@@](C)(CC=C(C)C)C1=O

InChI Identifier

InChI=1S/C26H38O5/c1-14(2)9-11-25(7)23(29)18(22(28)20(24(25)30)21(27)16(5)6)13-19-17(15(3)4)10-12-26(19,8)31/h9,16-17,19,28-29,31H,3,10-13H2,1-2,4-8H3/t17-,19-,25+,26+/m0/s1

InChI Key

QYPGFMLLGVPVHG-IPFQZCJUSA-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
Hypericum henryi	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monocyclic monoterpenoids. These are monoterpenoids containing 1 ring in the isoprene chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Monocyclic monoterpenoids

Alternative Parents

Substituents

Monocyclic monoterpenoid
Cyclopentanol
Vinylogous acid
Tertiary alcohol
Cyclic alcohol
Cyclic ketone
Ketone
Enol
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic 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	4.74	ChemAxon
pKa (Strongest Acidic)	4.54	ChemAxon
pKa (Strongest Basic)	-0.67	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	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

8585892

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10410455

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one (NP0213385)

MOL for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

3D MOL for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

3D SDF for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

3D-SDF for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

PDB for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

3D PDB for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

SMILES for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

INCHI for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

Structure for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)

3D Structure for NP0213385 ((6r)-3,5-dihydroxy-4-{[(1s,2r,5r)-2-hydroxy-2-methyl-5-(prop-1-en-2-yl)cyclopentyl]methyl}-6-methyl-6-(3-methylbut-2-en-1-yl)-2-(2-methylpropanoyl)cyclohexa-2,4-dien-1-one)