NP-MRD: Showing NP-Card for (3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one (NP0169047)

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Record Information

Version

1.0

Created at

2022-09-03 04:56:20 UTC

Updated at

2022-09-03 04:56:20 UTC

NP-MRD ID

NP0169047

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one

Description

(3S)-5-hydroxy-3-[(2R,6S)-6-hydroxy-5-[(7E)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2H-pyran-2-yl]-3,4-dihydro-2H-pyrrol-2-one belongs to the class of organic compounds known as diterpenoids. These are terpene compounds formed by four isoprene units. (3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one is found in Hippospongia lachne. Based on a literature review very few articles have been published on (3S)-5-hydroxy-3-[(2R,6S)-6-hydroxy-5-[(7E)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2H-pyran-2-yl]-3,4-dihydro-2H-pyrrol-2-one.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309032206562D          

 30 31  0  0  1  0            999 V2000
    3.5724   14.1911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   13.3661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   12.9536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   12.9536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   12.1286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   11.7161    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   10.8911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   10.4786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    9.6536    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

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M  END


  Mrv1652309032206562D          

 30 31  0  0  1  0            999 V2000
    3.5724   14.1911    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0169047

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC\C(C)=C\CCC(C)=CCCC1=CC[C@@H](O[C@@H]1O)[C@@H]1CC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H37NO4/c1-17(2)8-5-9-18(3)10-6-11-19(4)12-7-13-20-14-15-22(30-25(20)29)21-16-23(27)26-24(21)28/h8,10,12,14,21-22,25,29H,5-7,9,11,13,15-16H2,1-4H3,(H,26,27,28)/b18-10+,19-12?/t21-,22+,25-/m0/s1

> <INCHI_KEY>
DHMXAXCAWHUFET-WCGJWLOESA-N

> <FORMULA>
C25H37NO4

> <MOLECULAR_WEIGHT>
415.574

> <EXACT_MASS>
415.272258675

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
67

> <JCHEM_AVERAGE_POLARIZABILITY>
49.430091967039345

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(3S)-5-hydroxy-3-[(2R,6S)-6-hydroxy-5-[(7E)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2H-pyran-2-yl]-3,4-dihydro-2H-pyrrol-2-one

> <ALOGPS_LOGP>
5.05

> <JCHEM_LOGP>
4.841770028666668

> <ALOGPS_LOGS>
-4.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.8480649151139

> <JCHEM_PKA_STRONGEST_ACIDIC>
5.626811170105361

> <JCHEM_PKA_STRONGEST_BASIC>
-3.698192098139154

> <JCHEM_POLAR_SURFACE_AREA>
79.12

> <JCHEM_REFRACTIVITY>
123.19799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.71e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3S)-5-hydroxy-3-[(2R,6S)-6-hydroxy-5-[(7E)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2H-pyran-2-yl]-3,4-dihydropyrrol-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 03-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-22         0                                  
HETATM    1  C   UNK     0       6.668  26.490   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.668  24.950   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002  24.180   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.335  24.180   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       5.335  22.640   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       4.001  21.870   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       4.001  20.330   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.335  19.560   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667  19.560   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  18.020   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.334  17.250   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.334  15.710   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667  14.940   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.000  14.940   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.000  13.400   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334  12.630   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       1.334  11.090   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.667  10.320   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.667   8.780   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.334   8.010   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.334   6.470   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.580   5.565   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.104   4.100   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       3.009   2.854   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0       0.564   4.100   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       0.088   5.565   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -1.377   6.041   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.000   8.780   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      -0.000  10.320   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      -1.334  11.090   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   29                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   21   27                                                  
CONECT   27   26                                                            
CONECT   28   20   29                                                       
CONECT   29   28   17   30                                                  
CONECT   30   29                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   62    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₅H₃₇NO₄

Average Mass

415.5740 Da

Monoisotopic Mass

415.27226 Da

IUPAC Name

(3S)-5-hydroxy-3-[(2R,6S)-6-hydroxy-5-[(7E)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2H-pyran-2-yl]-3,4-dihydro-2H-pyrrol-2-one

Traditional Name

(3S)-5-hydroxy-3-[(2R,6S)-6-hydroxy-5-[(7E)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2H-pyran-2-yl]-3,4-dihydropyrrol-2-one

CAS Registry Number

Not Available

SMILES

CC(C)=CCC\C(C)=C\CCC(C)=CCCC1=CC[C@@H](O[C@@H]1O)[C@@H]1CC(O)=NC1=O

InChI Identifier

InChI=1S/C25H37NO4/c1-17(2)8-5-9-18(3)10-6-11-19(4)12-7-13-20-14-15-22(30-25(20)29)21-16-23(27)26-24(21)28/h8,10,12,14,21-22,25,29H,5-7,9,11,13,15-16H2,1-4H3,(H,26,27,28)/b18-10+,19-12?/t21-,22+,25-/m0/s1

InChI Key

DHMXAXCAWHUFET-WCGJWLOESA-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
Hippospongia lachne	LOTUS Database	35616633

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

Diterpenoid
Pyran
Pyrroline
Lactim
N-acylimine
Hemiacetal
Oxacycle
Azacycle
Organoheterocyclic compound
Organic 1,3-dipolar compound
Propargyl-type 1,3-dipolar organic compound
Carboxylic acid derivative
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
Carbonyl group
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic 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	5.05	ALOGPS
logP	4.84	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	5.63	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	79.12 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	123.2 m³·mol⁻¹	ChemAxon
Polarizability	49.43 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

162945829

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-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one (NP0169047)

MOL for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

3D MOL for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

3D SDF for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

3D-SDF for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

PDB for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

3D PDB for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

SMILES for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

INCHI for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

Structure for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)

3D Structure for NP0169047 ((3s)-5-hydroxy-3-[(2r,6s)-6-hydroxy-5-[(7e)-4,8,12-trimethyltrideca-3,7,11-trien-1-yl]-3,6-dihydro-2h-pyran-2-yl]-3,4-dihydropyrrol-2-one)