NP-MRD: Showing NP-Card for (1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione (NP0288723)

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Record Information

Version

2.0

Created at

2022-09-09 18:33:02 UTC

Updated at

2022-09-09 18:33:02 UTC

NP-MRD ID

NP0288723

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione

Description

Stigmastane-3,6-dione belongs to the class of organic compounds known as stigmastanes and derivatives. These are sterol lipids with a structure based on the stigmastane skeleton, which consists of a cholestane moiety bearing an ethyl group at the carbon atom C24. Thus, stigmastane-3,6-dione is considered to be a sterol. (1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione is found in Annona ambotay, Brucea javanica, Conium maculatum, Gleditsia sinensis, Houttuynia cordata, Larix kaempferi and Macaranga tanarius. (1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione was first documented in 2004 (PMID: 14971021). Based on a literature review a significant number of articles have been published on Stigmastane-3,6-dione (PMID: 31148485) (PMID: 27350550) (PMID: 34570603) (PMID: 23148482) (PMID: 35515514) (PMID: 33307809).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652309092220332D          

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M  END

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  Mrv1652309092220332D          

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 14 15  2  0  0  0  0
 16 14  1  1  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 16 22  1  0  0  0  0
 22 23  1  1  0  0  0
 22 24  1  0  0  0  0
 12 24  1  0  0  0  0
 24 25  1  1  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 11 27  1  0  0  0  0
  8 27  1  0  0  0  0
 27 28  1  1  0  0  0
  3 29  1  0  0  0  0
 29 30  1  0  0  0  0
 29 31  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0288723

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC[C@H](CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC(=O)[C@H]4CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C)C(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C29H48O2/c1-7-20(18(2)3)9-8-19(4)23-10-11-24-22-17-27(31)26-16-21(30)12-14-29(26,6)25(22)13-15-28(23,24)5/h18-20,22-26H,7-17H2,1-6H3/t19-,20-,22+,23-,24+,25+,26-,28-,29-/m1/s1

> <INCHI_KEY>
HMMVBUVVQLUGQA-UMQMBAGDSA-N

> <FORMULA>
C29H48O2

> <MOLECULAR_WEIGHT>
428.701

> <EXACT_MASS>
428.365430786

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
79

> <JCHEM_AVERAGE_POLARIZABILITY>
54.099756659339334

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,7S,10S,11S,14R,15R)-14-[(2R,5R)-5-ethyl-6-methylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8-dione

> <JCHEM_LOGP>
7.534306531666669

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.767757604997048

> <JCHEM_PKA_STRONGEST_BASIC>
-7.095221451736972

> <JCHEM_POLAR_SURFACE_AREA>
34.14

> <JCHEM_REFRACTIVITY>
128.55529999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,7S,10S,11S,14R,15R)-14-[(2R,5R)-5-ethyl-6-methylheptan-2-yl]-2,15-dimethyltetracyclo[8.7.0.0^{2,7}.0^{11,15}]heptadecane-5,8-dione

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 09-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-SEP-22         0                                  
HETATM    1  C   UNK     0      15.479  -0.353   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.939  -0.353   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      13.169  -1.687   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.629  -1.687   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.859  -3.020   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.319  -3.020   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.549  -4.354   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       8.549  -1.687   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.018  -1.526   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.697  -0.019   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       8.031   0.751   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.351   2.257   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.207   3.288   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.527   4.794   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       6.383   5.824   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       8.992   5.270   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       9.312   6.776   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      10.776   7.252   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      11.097   8.758   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      11.921   6.222   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      11.601   4.715   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      10.136   4.239   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      11.281   3.209   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       9.816   2.733   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.960   1.702   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.640   0.196   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.176  -0.280   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      10.206  -1.424   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      13.939  -3.020   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      15.479  -3.020   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      13.169  -4.354   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   29                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9   27                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   27                                                  
CONECT   12   11   13   24                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   22                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   16   23   24                                             
CONECT   23   22                                                            
CONECT   24   22   12   25                                                  
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   11    8   28                                             
CONECT   28   27                                                            
CONECT   29    3   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   68    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₂₉H₄₈O₂

Average Mass

428.7010 Da

Monoisotopic Mass

428.36543 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CC[C@H](CC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CC(=O)[C@H]4CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C)C(C)C

InChI Identifier

InChI=1S/C29H48O2/c1-7-20(18(2)3)9-8-19(4)23-10-11-24-22-17-27(31)26-16-21(30)12-14-29(26,6)25(22)13-15-28(23,24)5/h18-20,22-26H,7-17H2,1-6H3/t19-,20-,22+,23-,24+,25+,26-,28-,29-/m1/s1

InChI Key

HMMVBUVVQLUGQA-UMQMBAGDSA-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
Annona ambotay	LOTUS Database	35616633
Brucea javanica	LOTUS Database	35616633
Conium maculatum	LOTUS Database	35616633
Gleditsia sinensis	LOTUS Database	35616633
Houttuynia cordata	LOTUS Database	35616633
Larix kaempferi	LOTUS Database	35616633
Macaranga tanarius	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as stigmastanes and derivatives. These are sterol lipids with a structure based on the stigmastane skeleton, which consists of a cholestane moiety bearing an ethyl group at the carbon atom C24.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Stigmastanes and derivatives

Direct Parent

Stigmastanes and derivatives

Alternative Parents

Substituents

Triterpenoid
Stigmastane-skeleton
Ecdysteroid
6-oxosteroid
3-oxo-5-alpha-steroid
Oxosteroid
3-oxosteroid
Cyclic ketone
Ketone
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00031395

Chemspider ID

20038712

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

13992092

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Yannick Stephane FF, Dawe A, Angelbert Fusi A, Jean Jules BK, Ulrich KKD, Lateef M, Bruno LN, Ali MS, Ngouela SA: Crotoliganfuran, a new clerodane-type furano-diterpenoid from Croton oligandrus Pierre ex Hutch. Nat Prod Res. 2021 Jan;35(1):63-71. doi: 10.1080/14786419.2019.1613399. Epub 2019 May 31. [PubMed:31148485 ]
Khedr AI, Ibrahim SR, Mohamed GA, Ahmed HE, Ahmad AS, Ramadan MA, El-Baky AE, Yamada K, Ross SA: New ursane triterpenoids from Ficus pandurata and their binding affinity for human cannabinoid and opioid receptors. Arch Pharm Res. 2016 Jul;39(7):897-911. doi: 10.1007/s12272-016-0784-y. Epub 2016 Jun 27. [PubMed:27350550 ]
Tchamadeu Keugwa CV, Essoung Ehawa FR, Mouthe Happi G, Dongmo Tekapi Tsopgni W, Kamdem Waffo AF, Ndom JC, Wansi JD: Three new 30-norfriedelane and a new friedelane triterpenes from the trunk bark of Caloncoba welwitschii (Oliv.) Gilg (Achariaceae). Nat Prod Res. 2021 Sep 27:1-10. doi: 10.1080/14786419.2021.1981314. [PubMed:34570603 ]
Szakiel A, Nizynski B, Paczkowski C: Triterpenoid profile of flower and leaf cuticular waxes of heather Calluna vulgaris. Nat Prod Res. 2013 Aug;27(15):1404-7. doi: 10.1080/14786419.2012.742083. Epub 2012 Nov 13. [PubMed:23148482 ]
Qiao YJ, Zhang JJ, Shang JH, Zhu HT, Wang D, Yang CR, Zhang YJ: GC-MS-based identification and statistical analysis of liposoluble components in the rhizosphere soils of Panax notoginseng. RSC Adv. 2019 Jul 2;9(36):20557-20564. doi: 10.1039/c9ra02110h. eCollection 2019 Jul 1. [PubMed:35515514 ]
Khatoon B, Zikr Ur Rehman S, Yousuf S, Lateef M, Essombo MFA, Kamdem Waffo AF, Ali MS: New bioactive monoterpene indole alkaloid from Rinorea yaundensis Engl. Nat Prod Res. 2022 Feb;36(4):942-951. doi: 10.1080/14786419.2020.1855160. Epub 2020 Dec 12. [PubMed:33307809 ]
Duarte N, Ramalhete C, Varga A, Molnar J, Ferreira MJ: Multidrug resistance modulation and apoptosis induction of cancer cells by terpenic compounds isolated from Euphorbia species. Anticancer Res. 2009 Nov;29(11):4467-72. [PubMed:20032393 ]
Zhao CC, Shao JH, Li X, Xu J, Zhang P: Antimicrobial constituents from fruits of Ailanthus altissima SWINGLE. Arch Pharm Res. 2005 Oct;28(10):1147-51. doi: 10.1007/BF02972977. [PubMed:16276970 ]
Lim JC, Park JH, Budesinsky M, Kasal A, Han YH, Koo BS, Lee SI, Lee DU: Antimutagenic constituents from the thorns of Gleditsia sinensis. Chem Pharm Bull (Tokyo). 2005 May;53(5):561-4. doi: 10.1248/cpb.53.561. [PubMed:15863930 ]
Wei K, Li W, Koike K, Pei Y, Chen Y, Nikaido T: Complete 1H and 13C NMR assignments of two phytosterols from roots of Piper nigrum. Magn Reson Chem. 2004 Mar;42(3):355-9. doi: 10.1002/mrc.1347. [PubMed:14971021 ]
LOTUS database [Link]

Showing NP-Card for (1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione (NP0288723)

MOL for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

3D MOL for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

3D SDF for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

3D-SDF for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

PDB for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

3D PDB for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

SMILES for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

INCHI for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

Structure for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)

3D Structure for NP0288723 ((1r,3as,3bs,5as,9ar,9bs,11ar)-1-[(2r,5r)-5-ethyl-6-methylheptan-2-yl]-9a,11a-dimethyl-dodecahydro-1h-cyclopenta[a]phenanthrene-5,7-dione)