NP-MRD: Showing NP-Card for (2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid (NP0322003)

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Record Information

Version

2.0

Created at

2022-09-12 00:30:50 UTC

Updated at

2022-09-12 00:30:51 UTC

NP-MRD ID

NP0322003

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid

Description

(2Z,6S)-6-[(1S,1'S,2S,3aR,3'aS,7aS,7'aS)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-hexadecahydro-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoic acid belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units. (2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid is found in Amphipterygium adstringens. Based on a literature review very few articles have been published on (2Z,6S)-6-[(1S,1'S,2S,3aR,3'aS,7aS,7'aS)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-hexadecahydro-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoic acid.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309122202302D          

 35 38  0  0  1  0            999 V2000
    8.2488    1.2589    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

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M  END


  Mrv1652309122202302D          

 35 38  0  0  1  0            999 V2000
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   -0.6347   -0.3515    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0968    0.5625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9080    0.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4388    1.1901    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2500    1.0401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5257    0.2625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9191    0.9877    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2126    0.2749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7808   -0.3233    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4105    0.0820    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  8  6  1  6  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  1  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 15 13  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
  8 18  1  0  0  0  0
 11 18  1  0  0  0  0
 18 19  1  6  0  0  0
 15 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 23 22  1  1  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
 24 26  1  0  0  0  0
 24 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
 30 31  1  0  0  0  0
 23 31  1  0  0  0  0
 15 31  1  0  0  0  0
 31 32  1  1  0  0  0
  2 33  1  0  0  0  0
 33 34  2  0  0  0  0
 33 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0322003

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H](CC\C=C(\C)C(O)=O)[C@@H]1CC[C@]2(C)C(=O)[C@]3(CC[C@@]12C)[C@@H](O)C[C@@H]1[C@]3(C)CCC(=O)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H46O5/c1-18(9-8-10-19(2)24(33)34)20-11-13-29(7)25(35)30(16-15-27(20,29)5)23(32)17-21-26(3,4)22(31)12-14-28(21,30)6/h10,18,20-21,23,32H,8-9,11-17H2,1-7H3,(H,33,34)/b19-10-/t18-,20-,21-,23-,27-,28-,29+,30-/m0/s1

> <INCHI_KEY>
NRHGLEFWYOMSMY-NBIZHPMCSA-N

> <FORMULA>
C30H46O5

> <MOLECULAR_WEIGHT>
486.693

> <EXACT_MASS>
486.334524581

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
81

> <JCHEM_AVERAGE_POLARIZABILITY>
56.94923147745965

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z,6S)-6-[(1S,1'S,2S,3aR,3'aS,7aS,7'aS)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-hexadecahydro-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoic acid

> <JCHEM_LOGP>
6.537998091000002

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
14.50560964728201

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.812292390999384

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0150438009801848

> <JCHEM_POLAR_SURFACE_AREA>
91.67

> <JCHEM_REFRACTIVITY>
137.0432

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2Z,6S)-6-[(1S,1'S,2S,3aR,3'aS,7aS,7'aS)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'H,2H-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 12-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-22         0                                  
HETATM    1  C   UNK     0      15.398   2.350   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.900   1.990   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.840   3.107   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.343   2.746   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.282   3.863   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.785   3.503   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.724   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.348   2.026   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.286   0.805   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       8.414  -0.465   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       6.937  -0.028   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.139  -1.555   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       5.625  -0.833   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       5.666  -2.373   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       4.271  -0.099   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       4.230   1.441   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.543   2.246   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.896   1.512   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       7.017   3.047   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.151  -1.634   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       4.956  -2.947   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0       2.654  -1.994   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.848  -0.681   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       0.334  -0.401   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.321  -1.941   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.185  -0.656   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.181   1.050   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      -1.695   1.330   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       0.819   2.221   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       2.333   1.941   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       2.848   0.490   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.582   1.844   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.464   0.513   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      14.524  -0.604   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      11.966   0.153   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   33                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   18                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   18                                             
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   20   31                                             
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17    8   11   19                                             
CONECT   19   18                                                            
CONECT   20   15   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24   31                                                  
CONECT   24   23   25   26   27                                             
CONECT   25   24                                                            
CONECT   26   24                                                            
CONECT   27   24   28   29                                                  
CONECT   28   27                                                            
CONECT   29   27   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   23   15   32                                             
CONECT   32   31                                                            
CONECT   33    2   34   35                                                  
CONECT   34   33                                                            
CONECT   35   33                                                            
MASTER        0    0    0    0    0    0    0    0   35    0   76    0
END

View in JSmol

Synonyms

Value	Source
(2Z,6S)-6-[(1S,1's,2S,3AR,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-hexadecahydro-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoate	Generator

Chemical Formula

C₃₀H₄₆O₅

Average Mass

486.6930 Da

Monoisotopic Mass

486.33452 Da

IUPAC Name

(2Z,6S)-6-[(1S,1'S,2S,3aR,3'aS,7aS,7'aS)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-hexadecahydro-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoic acid

Traditional Name

(2Z,6S)-6-[(1S,1'S,2S,3aR,3'aS,7aS,7'aS)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'H,2H-1,5'-spirobi[indene]-1'-yl]-2-methylhept-2-enoic acid

CAS Registry Number

Not Available

SMILES

C[C@@H](CC\C=C(\C)C(O)=O)[C@@H]1CC[C@]2(C)C(=O)[C@]3(CC[C@@]12C)[C@@H](O)C[C@@H]1[C@]3(C)CCC(=O)C1(C)C

InChI Identifier

InChI=1S/C30H46O5/c1-18(9-8-10-19(2)24(33)34)20-11-13-29(7)25(35)30(16-15-27(20,29)5)23(32)17-21-26(3,4)22(31)12-14-28(21,30)6/h10,18,20-21,23,32H,8-9,11-17H2,1-7H3,(H,33,34)/b19-10-/t18-,20-,21-,23-,27-,28-,29+,30-/m0/s1

InChI Key

NRHGLEFWYOMSMY-NBIZHPMCSA-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
Amphipterygium adstringens	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sesquiterpenoids. These are terpenes with three consecutive isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Sesquiterpenoids

Direct Parent

Sesquiterpenoids

Alternative Parents

Substituents

Sesquiterpenoid
Medium-chain fatty acid
Branched fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Fatty acid
Unsaturated fatty acid
Cyclic alcohol
Ketone
Secondary alcohol
Cyclic ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Alcohol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organooxygen compound
Organic oxygen 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	6.54	ChemAxon
pKa (Strongest Acidic)	4.81	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	91.67 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	137.04 m³·mol⁻¹	ChemAxon
Polarizability	56.95 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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

162930885

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid (NP0322003)

MOL for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

3D MOL for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

3D SDF for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

3D-SDF for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

PDB for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

3D PDB for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

SMILES for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

INCHI for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

Structure for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)

3D Structure for NP0322003 ((2z,6s)-6-[(1s,1's,2s,3ar,3'as,7as,7'as)-2-hydroxy-3'a,4,4,7a,7'a-pentamethyl-4',5-dioxo-octahydro-1'h,2h-1,5'-spirobi[inden]-1'-yl]-2-methylhept-2-enoic acid)