NP-MRD: Showing NP-Card for 3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid (NP0157694)

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Record Information

Version

2.0

Created at

2022-09-02 15:08:24 UTC

Updated at

2022-09-02 15:08:24 UTC

NP-MRD ID

NP0157694

Secondary Accession Numbers

None

Natural Product Identification

Common Name

3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid

Description

Atomaric acid, also known as atomarate, belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other. 3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid is found in Stypopodium zonale and Taonia atomaria. 3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid was first documented in 2002 (PMID: 12444716). Based on a literature review a small amount of articles have been published on atomaric acid (PMID: 27618071) (PMID: 21986522) (PMID: 17713872).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309022217082D          

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M  END

     RDKit          3D

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M  END


  Mrv1652309022217082D          

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 17 31  1  0  0  0  0
  9 32  2  0  0  0  0
  3 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0157694

> <DATABASE_NAME>
NP-MRD

> <SMILES>
COC1=CC(C)=C(O)C(C[C@@]2(C)[C@H](C)CC[C@@]3(C)[C@H](CCC(O)=O)C(CC[C@H]23)=C(C)C)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C28H42O4/c1-17(2)22-8-10-24-27(5,23(22)9-11-25(29)30)13-12-19(4)28(24,6)16-20-15-21(32-7)14-18(3)26(20)31/h14-15,19,23-24,31H,8-13,16H2,1-7H3,(H,29,30)/t19-,23-,24+,27+,28+/m1/s1

> <INCHI_KEY>
OZFVNSYPXRUABC-CDFQXQCSSA-N

> <FORMULA>
C28H42O4

> <MOLECULAR_WEIGHT>
442.64

> <EXACT_MASS>
442.308309832

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
74

> <JCHEM_AVERAGE_POLARIZABILITY>
52.524656911856745

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-[(1S,4aR,5S,6R,8aR)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-decahydronaphthalen-1-yl]propanoic acid

> <ALOGPS_LOGP>
5.83

> <JCHEM_LOGP>
6.896835695333335

> <ALOGPS_LOGS>
-5.72

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.56902408816385

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.865336592976854

> <JCHEM_PKA_STRONGEST_BASIC>
-4.81063176183171

> <JCHEM_POLAR_SURFACE_AREA>
66.76

> <JCHEM_REFRACTIVITY>
130.02929999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.44e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-[(1S,4aR,5S,6R,8aR)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1H-naphthalen-1-yl]propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 02-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   02-SEP-22         0                                  
HETATM    1  C   UNK     0       6.291  -9.136   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       5.764  -7.689   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       4.247  -7.421   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.258  -8.601   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.741  -8.334   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.751  -9.513   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.214  -6.887   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -0.302  -6.619   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       2.204  -5.707   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.677  -4.260   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -3.080   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.657  -4.260   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000  -3.080   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0       6.668  -0.770   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       8.002  -0.000   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.336  -0.770   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.002   1.540   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       6.668  -2.310   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.335  -3.080   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.001  -2.310   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.721  -5.974   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   32                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10   32                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13   31                                             
CONECT   12   11                                                            
CONECT   13   11   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19   31                                             
CONECT   18   17                                                            
CONECT   19   17   20   25                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   19   26   29                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   25   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   11   17                                                  
CONECT   32    9    3                                                       
MASTER        0    0    0    0    0    0    0    0   32    0   68    0
END

View in JSmol

Synonyms

Value	Source
Atomarate	Generator

Chemical Formula

C₂₈H₄₂O₄

Average Mass

442.6400 Da

Monoisotopic Mass

442.30831 Da

IUPAC Name

3-[(1S,4aR,5S,6R,8aR)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-decahydronaphthalen-1-yl]propanoic acid

Traditional Name

3-[(1S,4aR,5S,6R,8aR)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1H-naphthalen-1-yl]propanoic acid

CAS Registry Number

Not Available

SMILES

COC1=CC(C)=C(O)C(C[C@@]2(C)[C@H](C)CC[C@@]3(C)[C@H](CCC(O)=O)C(CC[C@H]23)=C(C)C)=C1

InChI Identifier

InChI=1S/C28H42O4/c1-17(2)22-8-10-24-27(5,23(22)9-11-25(29)30)13-12-19(4)28(24,6)16-20-15-21(32-7)14-18(3)26(20)31/h14-15,19,23-24,31H,8-13,16H2,1-7H3,(H,29,30)/t19-,23-,24+,27+,28+/m1/s1

InChI Key

OZFVNSYPXRUABC-CDFQXQCSSA-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
Stypopodium zonale	LOTUS Database	35616633
Taonia atomaria	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as bicyclic monoterpenoids. These are monoterpenoids containing exactly 2 rings, which are fused to each other.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Monoterpenoids

Direct Parent

Bicyclic monoterpenoids

Alternative Parents

Substituents

Aromatic monoterpenoid
Bicyclic monoterpenoid
Methoxyphenol
4-alkoxyphenol
Carbocyclic fatty acid
Phenoxy compound
Anisole
Methoxybenzene
Phenol ether
O-cresol
Alkyl aryl ether
Toluene
Phenol
Hydroxy fatty acid
Monocyclic benzene moiety
Fatty acyl
Benzenoid
Carboxylic acid
Carboxylic acid derivative
Ether
Monocarboxylic acid or derivatives
Carbonyl group
Organic oxide
Organic oxygen compound
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	5.83	ALOGPS
logP	6.9	ChemAxon
logS	-5.7	ALOGPS
pKa (Strongest Acidic)	4.87	ChemAxon
pKa (Strongest Basic)	-4.8	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	66.76 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	130.03 m³·mol⁻¹	ChemAxon
Polarizability	52.52 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00045673

Chemspider ID

10476761

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21774685

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Soares DC, Szlachta MM, Teixeira VL, Soares AR, Saraiva EM: The Brown Alga Stypopodium zonale (Dictyotaceae): A Potential Source of Anti-Leishmania Drugs. Mar Drugs. 2016 Sep 8;14(9). pii: md14090163. doi: 10.3390/md14090163. [PubMed:27618071 ]
Mendes G, Soares AR, Sigiliano L, Machado F, Kaiser C, Romeiro N, Gestinari L, Santos N, Romanos MT: In vitro anti-HMPV activity of meroditerpenoids from marine alga Stypopodium zonale (Dictyotales). Molecules. 2011 Oct 10;16(10):8437-50. doi: 10.3390/molecules16108437. [PubMed:21986522 ]
Soares AR, Abrantes JL, Lopes Souza TM, Leite Fontes CF, Pereira RC, de Palmer Paixao Frugulhetti IC, Teixeira VL: In vitro antiviral effect of meroditerpenes isolated from the Brazilian seaweed Stypopodium zonale (Dictyotales). Planta Med. 2007 Sep;73(11):1221-4. doi: 10.1055/s-2007-981589. Epub 2007 Aug 23. [PubMed:17713872 ]
Dorta E, Cueto M, Brito I, Darias J: New terpenoids from the brown alga Stypopodium zonale. J Nat Prod. 2002 Nov;65(11):1727-30. doi: 10.1021/np020090g. [PubMed:12444716 ]
LOTUS database [Link]

Showing NP-Card for 3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid (NP0157694)

MOL for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

3D MOL for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

3D SDF for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

3D-SDF for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

PDB for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

3D PDB for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

SMILES for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

INCHI for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

Structure for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)

3D Structure for NP0157694 (3-[(1s,4ar,5s,6r,8ar)-5-[(2-hydroxy-5-methoxy-3-methylphenyl)methyl]-5,6,8a-trimethyl-2-(propan-2-ylidene)-hexahydro-1h-naphthalen-1-yl]propanoic acid)