NP-MRD: Showing NP-Card for cimigenol (NP0152463)

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Record Information

Version

2.0

Created at

2022-09-02 08:56:24 UTC

Updated at

2022-09-02 08:56:24 UTC

NP-MRD ID

NP0152463

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cimigenol

Description

Cimigenol belongs to the class of organic compounds known as cycloartanols and derivatives. These are steroids containing a cycloartanol moiety. Thus, cimigenol is considered to be a sterol. cimigenol is found in Actaea japonica, Actaea pachypoda and Actaea yunnanensis. cimigenol was first documented in 2017 (PMID: 28374633). Based on a literature review a small amount of articles have been published on cimigenol (PMID: 32053921) (PMID: 30584366) (PMID: 30486523) (PMID: 28260002).

Structure

MOL 3D MOL SDF PDB SMILES InChI

  Mrv1652309022210562D          

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M  END

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M  END

  Mrv1652309022210562D          

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    4.6355    2.4379    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.9430    3.2035    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4679    2.4707    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  1  0  0  0
  6  5  1  1  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  1  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  1  0  0  0  0
  6 13  1  0  0  0  0
 13 14  1  6  0  0  0
 13 15  1  0  0  0  0
 15 16  1  6  0  0  0
 15 17  1  0  0  0  0
 17 18  1  6  0  0  0
 18 19  1  0  0  0  0
 20 19  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 21 24  1  0  0  0  0
 24 25  1  1  0  0  0
 24 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 20 28  1  0  0  0  0
 28 29  1  1  0  0  0
 30 29  1  1  0  0  0
 17 30  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 15 33  1  0  0  0  0
 33 34  1  1  0  0  0
 35 33  1  1  0  0  0
  2 35  1  0  0  0  0
  6 35  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0152463

> <DATABASE_NAME>
NP-MRD

> <SMILES>
C[C@@H]1C[C@H]2O[C@@]3(O[C@@H]2C(C)(C)O)[C@H](O)[C@@]2(C)[C@@H]4CC[C@@H]5[C@]6(C[C@@]46CC[C@]2(C)[C@@H]13)CC[C@H](O)C5(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C30H48O5/c1-16-14-17-22(25(4,5)33)35-30(34-17)21(16)26(6)12-13-29-15-28(29)11-10-20(31)24(2,3)18(28)8-9-19(29)27(26,7)23(30)32/h16-23,31-33H,8-15H2,1-7H3/t16-,17-,18+,19+,20+,21-,22+,23-,26-,27-,28-,29+,30+/m1/s1

> <INCHI_KEY>
CNBHUROFMYCHGI-IEUUZZHOSA-N

> <FORMULA>
C30H48O5

> <MOLECULAR_WEIGHT>
488.709

> <EXACT_MASS>
488.350174646

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
83

> <JCHEM_AVERAGE_POLARIZABILITY>
57.0604978214856

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2R,3S,4R,7R,9S,12R,14S,17R,18R,19R,21R,22S)-22-(2-hydroxypropan-2-yl)-3,8,8,17,19-pentamethyl-23,24-dioxaheptacyclo[19.2.1.0^{1,18}.0^{3,17}.0^{4,14}.0^{7,12}.0^{12,14}]tetracosane-2,9-diol

> <ALOGPS_LOGP>
3.60

> <JCHEM_LOGP>
4.123931387666666

> <ALOGPS_LOGS>
-5.15

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.254507349520058

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.837798035041335

> <JCHEM_PKA_STRONGEST_BASIC>
-0.8348987776729729

> <JCHEM_POLAR_SURFACE_AREA>
79.15

> <JCHEM_REFRACTIVITY>
133.04460000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.46e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2R,3S,4R,7R,9S,12R,14S,17R,18R,19R,21R,22S)-22-(2-hydroxypropan-2-yl)-3,8,8,17,19-pentamethyl-23,24-dioxaheptacyclo[19.2.1.0^{1,18}.0^{3,17}.0^{4,14}.0^{7,12}.0^{12,14}]tetracosane-2,9-diol

> <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      10.547   7.356   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      11.144   5.936   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.720   5.685   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      13.285   4.179   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      11.987   3.679   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      10.812   3.069   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      12.010   1.892   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0      13.490   2.581   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      14.838   1.838   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      16.187   1.094   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      15.582   3.186   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      14.095   0.489   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       9.499   2.183   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0       9.491   0.643   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0       8.220   3.065   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       7.941   1.551   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.724   2.699   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.293   1.221   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       4.797   0.855   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       3.732   1.968   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.236   1.602   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.857   0.192   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       0.956   0.746   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0       1.171   2.714   0.000  0.00  0.00           C+0
HETATM   25  O   UNK     0      -0.324   2.348   0.000  0.00  0.00           O+0
HETATM   26  C   UNK     0       1.602   4.192   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       3.098   4.558   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.163   3.446   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       4.594   4.924   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.659   3.812   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.090   5.290   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       7.586   5.656   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       8.653   4.551   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       9.227   5.980   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      10.207   4.612   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   13   35                                             
CONECT    7    6    8                                                       
CONECT    8    7    4    9                                                  
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13    6   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13   16   17   33                                             
CONECT   16   15                                                            
CONECT   17   15   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   28                                                  
CONECT   21   20   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   20   29   30                                             
CONECT   29   28   30                                                       
CONECT   30   29   17   28   31                                             
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   15   34   35                                             
CONECT   34   33                                                            
CONECT   35   33    2    6                                                  
MASTER        0    0    0    0    0    0    0    0   35    0   82    0
END

View in JSmol

Synonyms

Value	Source
(23R,24S)-16,23-16,24-Diepoxy-9,19-cyclolanostan-3beta,15alpha,25-triol	MeSH

Chemical Formula

C₃₀H₄₈O₅

Average Mass

488.7090 Da

Monoisotopic Mass

488.35017 Da

IUPAC Name

(1S,2R,3S,4R,7R,9S,12R,14S,17R,18R,19R,21R,22S)-22-(2-hydroxypropan-2-yl)-3,8,8,17,19-pentamethyl-23,24-dioxaheptacyclo[19.2.1.0^{1,18}.0^{3,17}.0^{4,14}.0^{7,12}.0^{12,14}]tetracosane-2,9-diol

Traditional Name

(1S,2R,3S,4R,7R,9S,12R,14S,17R,18R,19R,21R,22S)-22-(2-hydroxypropan-2-yl)-3,8,8,17,19-pentamethyl-23,24-dioxaheptacyclo[19.2.1.0^{1,18}.0^{3,17}.0^{4,14}.0^{7,12}.0^{12,14}]tetracosane-2,9-diol

CAS Registry Number

Not Available

SMILES

C[C@@H]1C[C@H]2O[C@@]3(O[C@@H]2C(C)(C)O)[C@H](O)[C@@]2(C)[C@@H]4CC[C@@H]5[C@]6(C[C@@]46CC[C@]2(C)[C@@H]13)CC[C@H](O)C5(C)C

InChI Identifier

InChI=1S/C30H48O5/c1-16-14-17-22(25(4,5)33)35-30(34-17)21(16)26(6)12-13-29-15-28(29)11-10-20(31)24(2,3)18(28)8-9-19(29)27(26,7)23(30)32/h16-23,31-33H,8-15H2,1-7H3/t16-,17-,18+,19+,20+,21-,22+,23-,26-,27-,28-,29+,30+/m1/s1

InChI Key

CNBHUROFMYCHGI-IEUUZZHOSA-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
Actaea japonica	LOTUS Database	35616633
Actaea pachypoda	LOTUS Database	35616633
Actaea yunnanensis	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as cycloartanols and derivatives. These are steroids containing a cycloartanol moiety.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Steroids and steroid derivatives

Sub Class

Cycloartanols and derivatives

Direct Parent

Cycloartanols and derivatives

Alternative Parents

Substituents

Cycloartanol-skeleton
9b,19-cyclo-lanostane-skeleton
Cycloartane-skeleton
Triterpenoid
3-hydroxysteroid
3-beta-hydroxysteroid
15-hydroxysteroid
Hydroxysteroid
Ketal
Oxepane
Oxane
Meta-dioxolane
Cyclic alcohol
Tertiary alcohol
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Acetal
Hydrocarbon derivative
Organic oxygen compound
Alcohol
Organooxygen compound
Aliphatic heteropolycyclic compound

Molecular Framework

Aliphatic heteropolycyclic compounds

External Descriptors

triterpenoid (CHEBI:37777 )
Cycloartanols and derivatives (LMST01100005 )

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	3.6	ALOGPS
logP	4.12	ChemAxon
logS	-5.2	ALOGPS
pKa (Strongest Acidic)	12.84	ChemAxon
pKa (Strongest Basic)	-0.83	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	79.15 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	133.04 m³·mol⁻¹	ChemAxon
Polarizability	57.06 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	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

C00024071

Chemspider ID

13148746

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

16020000

PDB ID

Not Available

ChEBI ID

37777

Good Scents ID

Not Available

References

General References

Johrer K, Stuppner H, Greil R, Cicek SS: Structure-Guided Identification of Black Cohosh (Actaea racemosa) Triterpenoids with In Vitro Activity against Multiple Myeloma. Molecules. 2020 Feb 11;25(4):766. doi: 10.3390/molecules25040766. [PubMed:32053921 ]
Li X, Wang W, Fan Y, Wei Y, Yu LQ, Wei JF, Wang YF: Anticancer efficiency of cycloartane triterpenoid derivatives isolated from Cimicifuga yunnanensis Hsiao on triple-negative breast cancer cells. Cancer Manag Res. 2018 Dec 6;10:6715-6729. doi: 10.2147/CMAR.S185387. eCollection 2018. [PubMed:30584366 ]
Xia HM, Dai YP, Sun LL: [Research progress on cycloartane triterpenoids of Actaea]. Zhongguo Zhong Yao Za Zhi. 2018 Oct;43(20):4000-4010. doi: 10.19540/j.cnki.cjcmm.20180703.011. [PubMed:30486523 ]
Wu HF, Li PF, Zhu YD, Zhang XP, Ma GX, Xu XD, Liu YL, Luo ZH, Chen DZ, Zou QY, Zhao ZJ: Soulieoside O, a new cyclolanostane triterpenoid glycoside from Souliea vaginata. J Asian Nat Prod Res. 2017 Dec;19(12):1177-1182. doi: 10.1080/10286020.2017.1307190. Epub 2017 Apr 4. [PubMed:28374633 ]
Dai X, Liu J, Nian Y, Qiu MH, Luo Y, Zhang J: A novel cycloartane triterpenoid from Cimicifuga induces apoptotic and autophagic cell death in human colon cancer HT-29 cells. Oncol Rep. 2017 Apr;37(4):2079-2086. doi: 10.3892/or.2017.5444. Epub 2017 Feb 14. [PubMed:28260002 ]
LOTUS database [Link]

Showing NP-Card for cimigenol (NP0152463)

MOL for NP0152463 (cimigenol)

3D MOL for NP0152463 (cimigenol)

3D SDF for NP0152463 (cimigenol)

3D-SDF for NP0152463 (cimigenol)

PDB for NP0152463 (cimigenol)

3D PDB for NP0152463 (cimigenol)

SMILES for NP0152463 (cimigenol)

INCHI for NP0152463 (cimigenol)

Structure for NP0152463 (cimigenol)

3D Structure for NP0152463 (cimigenol)