NP-MRD: Showing NP-Card for (3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid (NP0307078)

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Record Information

Version

2.0

Created at

2022-09-10 23:57:41 UTC

Updated at

2022-09-10 23:57:41 UTC

NP-MRD ID

NP0307078

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid

Description

(3S)-5-[(1S,4aR,5R,8aR)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpentanoic acid belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. Based on a literature review very few articles have been published on (3S)-5-[(1S,4aR,5R,8aR)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpentanoic acid.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652309112201572D          

 23 24  0  0  1  0            999 V2000
    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    1.6500    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.6165    2.3317    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1468    3.2502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3343    3.3935    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.2868   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4302    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  5  4  1  1  0  0  0
  5  6  1  0  0  0  0
  6  7  1  1  0  0  0
  6  8  1  6  0  0  0
  8  9  1  0  0  0  0
  6 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
  5 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  2 15  1  0  0  0  0
 15 16  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  1  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0307078

> <DATABASE_NAME>
NP-MRD

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

> <INCHI_IDENTIFIER>
InChI=1S/C20H34O3/c1-14(12-18(22)23)6-8-16-15(2)7-9-17-19(3,13-21)10-5-11-20(16,17)4/h14,16-17,21H,2,5-13H2,1,3-4H3,(H,22,23)/t14-,16-,17-,19-,20+/m0/s1

> <INCHI_KEY>
KPFWQGCQQPFNRP-ABWNYZJXSA-N

> <FORMULA>
C20H34O3

> <MOLECULAR_WEIGHT>
322.489

> <EXACT_MASS>
322.250794955

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
57

> <JCHEM_AVERAGE_POLARIZABILITY>
38.23241410477688

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S)-5-[(1S,4aR,5R,8aR)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpentanoic acid

> <JCHEM_LOGP>
4.2446481626666674

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
18.592337012048223

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.718338199565721

> <JCHEM_PKA_STRONGEST_BASIC>
-1.227512282895515

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
92.86919999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-5-[(1S,4aR,5R,8aR)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1H-naphthalen-1-yl]-3-methylpentanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 11-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   11-SEP-22         0                                  
HETATM    1  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   3.080   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.151   4.353   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       2.141   6.067   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.624   6.335   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       4.001   5.390   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   4.620   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.335   3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.668   0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       8.002   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       8.002  -1.540   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.336   0.770   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.669   0.000   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      12.003   0.770   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      10.669  -1.540   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7    8   10                                             
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8                                                            
CONECT   10    6   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12    5   14   15                                             
CONECT   14   13                                                            
CONECT   15   13    2   16                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22   23                                                  
CONECT   22   21                                                            
CONECT   23   21                                                            
MASTER        0    0    0    0    0    0    0    0   23    0   48    0
END

View in JSmol

Synonyms

Value	Source
(3S)-5-[(1S,4AR,5R,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpentanoate	Generator

Chemical Formula

C₂₀H₃₄O₃

Average Mass

322.4890 Da

Monoisotopic Mass

322.25079 Da

IUPAC Name

(3S)-5-[(1S,4aR,5R,8aR)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-decahydronaphthalen-1-yl]-3-methylpentanoic acid

Traditional Name

(3S)-5-[(1S,4aR,5R,8aR)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1H-naphthalen-1-yl]-3-methylpentanoic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C20H34O3/c1-14(12-18(22)23)6-8-16-15(2)7-9-17-19(3,13-21)10-5-11-20(16,17)4/h14,16-17,21H,2,5-13H2,1,3-4H3,(H,22,23)/t14-,16-,17-,19-,20+/m0/s1

InChI Key

KPFWQGCQQPFNRP-ABWNYZJXSA-N

Experimental Spectra

Not Available

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Diterpenoids

Direct Parent

Diterpenoids

Alternative Parents

Substituents

Labdane diterpenoid
Diterpenoid
Carbocyclic fatty acid
Medium-chain hydroxy acid
Medium-chain fatty acid
Branched fatty acid
Hydroxy fatty acid
Methyl-branched fatty acid
Fatty acyl
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Carbonyl group
Organic oxygen compound
Organooxygen compound
Primary alcohol
Alcohol
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	4.24	ChemAxon
pKa (Strongest Acidic)	4.72	ChemAxon
pKa (Strongest Basic)	-1.2	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	6	ChemAxon
Refractivity	92.87 m³·mol⁻¹	ChemAxon
Polarizability	38.23 Å³	ChemAxon
Number of Rings	2	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

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

162979165

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

LOTUS database [Link]

Showing NP-Card for (3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid (NP0307078)

MOL for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

3D MOL for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

3D SDF for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

3D-SDF for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

PDB for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

3D PDB for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

SMILES for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

INCHI for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

Structure for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)

3D Structure for NP0307078 ((3s)-5-[(1s,4ar,5r,8ar)-5-(hydroxymethyl)-5,8a-dimethyl-2-methylidene-hexahydro-1h-naphthalen-1-yl]-3-methylpentanoic acid)