NP-MRD: Showing NP-Card for (1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid (NP0268872)

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Record Information

Version

2.0

Created at

2022-09-08 14:08:34 UTC

Updated at

2022-09-08 14:08:35 UTC

NP-MRD ID

NP0268872

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid

Description

Ryomenin belongs to the class of organic compounds known as naphthalenecarboxylic acids. Naphthalenecarboxylic acids are compounds containing a naphthalene moiety, which bears a carboxylic acid group one or more positions. Naphthalene is a bicyclic compound that is made up of two fused benzene ring. (1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid is found in Arachniodes mutica. Based on a literature review very few articles have been published on Ryomenin.

Structure

MOL 3D MOL SDF PDB SMILES InChI

     RDKit          3D

 36 38  0  0  0  0  0  0  0  0999 V2000
    3.4247   -1.0193    0.0112 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2860   -0.1707   -0.4970 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3695    1.2425   -0.0118 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1259    2.0243   -0.4600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0271    1.4867    0.3652 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1001    0.0155    0.1171 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3825   -0.4017    0.3306 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6066   -1.7482    0.1669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9219   -2.3308    0.3633 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9245   -1.6353    0.6933 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0915   -3.6993    0.1841 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5433   -2.5837   -0.1986 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7497   -2.1233   -0.4105 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8095   -2.9227   -0.7705 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9723   -0.7512   -0.2423 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2329    0.7684    0.6511 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3976    1.8813   -0.0756 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8327    3.2329    0.3675 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2133   -1.5156    0.9598 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7767   -1.6740   -0.7960 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2763   -0.3065    0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4064   -0.1376   -1.6244 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2775    1.2021    1.1113 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2901    1.7609   -0.3213 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9286    1.9354   -1.5271 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2817    3.0736   -0.1613 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0950    1.7285    1.4337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3999   -3.9986   -0.7298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7090   -3.6456   -0.3294 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6670   -3.9117   -0.8957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1944    1.0402    1.7265 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2361    0.7231    0.2297 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5490    1.6741   -1.1503 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3799    3.2318    1.3268 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9278    3.8983    0.3908 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4936    3.6561   -0.4431 H   0  0  0  0  0  0  0  0  0  0  0  0
 18 17  1  0
 17 16  1  0
 16  7  1  0
  7  6  2  0
  6  5  1  0
  5  4  1  0
  4  3  1  0
  3  2  1  0
  2  1  1  0
  2 15  1  0
 15 13  2  0
 13 14  1  0
 13 12  1  0
 12  8  2  0
  8  9  1  0
  9 11  1  0
  9 10  2  0
  5 17  1  0
  8  7  1  0
 15  6  1  0
 18 34  1  0
 18 35  1  0
 18 36  1  0
 17 33  1  6
 16 31  1  0
 16 32  1  0
  5 27  1  1
  4 25  1  0
  4 26  1  0
  3 23  1  0
  3 24  1  0
  2 22  1  6
  1 19  1  0
  1 20  1  0
  1 21  1  0
 14 30  1  0
 12 29  1  0
 11 28  1  0
M  END


  Mrv1652309082216082D          

 18 20  0  0  1  0            999 V2000
   -0.0009    0.8340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0853    0.0135    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5821   -0.4714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4959   -1.2919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2578   -1.6275    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.9252   -1.1425    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5926   -1.6275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3463   -1.2919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0138   -1.7768    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7674   -1.4413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9275   -2.5973    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4326   -0.4714    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7651    0.0135    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8805    0.8304    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8390   -0.3220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3377   -2.4121    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5127   -2.4121    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0278   -3.0795    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  6  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  2  0  0  0  0
  6 15  1  0  0  0  0
  2 15  1  0  0  0  0
  7 16  1  0  0  0  0
 16 17  1  0  0  0  0
  5 17  1  0  0  0  0
 17 18  1  1  0  0  0
M  END
> <DATABASE_ID>
NP0268872

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1CC2=C3[C@H]1CC[C@@H](C)C3=C(O)C=C2C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H18O3/c1-7-3-4-9-8(2)5-10-11(15(17)18)6-12(16)13(7)14(9)10/h6-9,16H,3-5H2,1-2H3,(H,17,18)/t7-,8-,9+/m1/s1

> <INCHI_KEY>
MLNIJTRDXCDNQZ-HLTSFMKQSA-N

> <FORMULA>
C15H18O3

> <MOLECULAR_WEIGHT>
246.306

> <EXACT_MASS>
246.12559444

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
36

> <JCHEM_AVERAGE_POLARIZABILITY>
27.24070548193086

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,6R,8aS)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid

> <JCHEM_LOGP>
3.6902703839999997

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.330231354196565

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.036634411695251

> <JCHEM_PKA_STRONGEST_BASIC>
-5.722998575712581

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
69.6621

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(1R,6R,8aS)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-SEP-22         0                                  
HETATM    1  C   UNK     0      -0.002   1.557   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.159   0.025   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.087  -0.880   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.926  -2.412   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.481  -3.038   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.727  -2.133   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.973  -3.038   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.380  -2.412   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.626  -3.317   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.033  -2.690   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       5.465  -4.848   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       4.541  -0.880   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       3.295   0.025   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       3.510   1.550   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       1.566  -0.601   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.497  -4.503   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.957  -4.503   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.052  -5.748   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   17                                                  
CONECT    6    5    7   15                                                  
CONECT    7    6    8   16                                                  
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6    2                                                  
CONECT   16    7   17                                                       
CONECT   17   16    5   18                                                  
CONECT   18   17                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   40    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₁₈O₃

Average Mass

246.3060 Da

Monoisotopic Mass

246.12559 Da

IUPAC Name

(1R,6R,8aS)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid

Traditional Name

(1R,6R,8aS)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid

CAS Registry Number

Not Available

SMILES

C[C@@H]1CC2=C3[C@H]1CC[C@@H](C)C3=C(O)C=C2C(O)=O

InChI Identifier

InChI=1S/C15H18O3/c1-7-3-4-9-8(2)5-10-11(15(17)18)6-12(16)13(7)14(9)10/h6-9,16H,3-5H2,1-2H3,(H,17,18)/t7-,8-,9+/m1/s1

InChI Key

MLNIJTRDXCDNQZ-HLTSFMKQSA-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
Arachniodes mutica	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as naphthalenecarboxylic acids. Naphthalenecarboxylic acids are compounds containing a naphthalene moiety, which bears a carboxylic acid group one or more positions. Naphthalene is a bicyclic compound that is made up of two fused benzene ring.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Naphthalenes

Sub Class

Naphthalenecarboxylic acids and derivatives

Direct Parent

Naphthalenecarboxylic acids

Alternative Parents

Substituents

2-naphthalenecarboxylic acid
Tetralin
Hydroxybenzoic acid
Indane
1-hydroxy-2-unsubstituted benzenoid
Phenol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aromatic homopolycyclic compound

Molecular Framework

Aromatic 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	3.69	ChemAxon
pKa (Strongest Acidic)	4.04	ChemAxon
pKa (Strongest Basic)	-5.7	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	57.53 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	69.66 m³·mol⁻¹	ChemAxon
Polarizability	27.24 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	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

C00020158

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

101614335

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid (NP0268872)

MOL for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

3D MOL for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

3D SDF for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

3D-SDF for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

PDB for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

3D PDB for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

SMILES for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

INCHI for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

Structure for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)

3D Structure for NP0268872 ((1r,6r,8as)-5-hydroxy-1,6-dimethyl-1,2,6,7,8,8a-hexahydroacenaphthylene-3-carboxylic acid)