NP-MRD: Showing NP-Card for cylindrin (NP0241176)

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Record Information

Version

2.0

Created at

2022-09-07 01:11:30 UTC

Updated at

2022-09-07 01:11:30 UTC

NP-MRD ID

NP0241176

Secondary Accession Numbers

None

Natural Product Identification

Common Name

cylindrin

Description

Cylindrin belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. cylindrin is found in Attalea cohune, Diospyros discolor, Diospyros nigra, Elaeis guineensis and Saccharum spontaneum. cylindrin was first documented in 2019 (PMID: 30854006). Based on a literature review a small amount of articles have been published on Cylindrin (PMID: 35917596) (PMID: 35718155) (PMID: 33621087) (PMID: 32659262).

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072203112D          

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     RDKit          3D

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 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  1  0  0  0
 17 18  1  0  0  0  0
 17 19  1  0  0  0  0
 16 20  1  0  0  0  0
 13 20  1  0  0  0  0
 20 21  1  1  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 11 24  1  0  0  0  0
 24 25  1  6  0  0  0
 24 26  1  0  0  0  0
 26  8  1  6  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 29 28  1  1  0  0  0
  6 29  1  0  0  0  0
 29 30  1  0  0  0  0
  3 30  1  0  0  0  0
 30 31  1  0  0  0  0
 30 32  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0241176

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CO[C@H]1CC[C@@]2(C)[C@@H](CC[C@@H]3C2=CC[C@]2(C)[C@H]4CC[C@@H](C(C)C)[C@]4(C)CC[C@@]32C)C1(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C31H52O/c1-20(2)21-10-13-25-29(21,6)18-19-30(7)23-11-12-24-27(3,4)26(32-9)15-16-28(24,5)22(23)14-17-31(25,30)8/h14,20-21,23-26H,10-13,15-19H2,1-9H3/t21-,23+,24-,25-,26-,28+,29-,30-,31+/m0/s1

> <INCHI_KEY>
MRNPHCMRIQYRFU-UWAWSDATSA-N

> <FORMULA>
C31H52O

> <MOLECULAR_WEIGHT>
440.756

> <EXACT_MASS>
440.401816294

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
84

> <JCHEM_AVERAGE_POLARIZABILITY>
56.84160848796341

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,2S,5S,6S,9S,10R,14S,17S,19R)-17-methoxy-2,5,10,14,18,18-hexamethyl-6-(propan-2-yl)pentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-ene

> <JCHEM_LOGP>
8.033239314333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-4.126415556826106

> <JCHEM_POLAR_SURFACE_AREA>
9.23

> <JCHEM_REFRACTIVITY>
136.732

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,2S,5S,6S,9S,10R,14S,17S,19R)-6-isopropyl-17-methoxy-2,5,10,14,18,18-hexamethylpentacyclo[11.8.0.0^{2,10}.0^{5,9}.0^{14,19}]henicos-12-ene

> <JCHEM_VEBER_RULE>
1

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  C   UNK     0       2.839  -5.242   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       3.589  -3.897   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       5.129  -3.873   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.878  -2.528   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.418  -2.505   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.208  -3.827   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       8.958  -2.481   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.748  -3.803   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.498  -2.458   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      12.037  -2.435   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.828  -3.756   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.577  -2.411   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.368  -3.733   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      15.380  -2.573   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      16.797  -3.178   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      16.659  -4.712   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      17.819  -5.725   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      19.276  -5.226   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      17.522  -7.236   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      15.158  -5.055   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      16.082  -6.287   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      14.408  -6.400   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.868  -6.423   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      12.078  -5.102   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.328  -6.447   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.538  -5.125   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.789  -6.470   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.249  -6.494   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.459  -5.172   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       5.919  -5.195   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       5.888  -6.735   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       4.625  -6.031   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   30                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8   29                                             
CONECT    7    6                                                            
CONECT    8    6    9   26                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   24                                             
CONECT   12   11                                                            
CONECT   13   11   14   20                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17   20                                                  
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17                                                            
CONECT   20   16   13   21   22                                             
CONECT   21   20                                                            
CONECT   22   20   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   11   25   26                                             
CONECT   25   24                                                            
CONECT   26   24    8   27                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28    6   30                                                  
CONECT   30   29    3   31   32                                             
CONECT   31   30                                                            
CONECT   32   30                                                            
MASTER        0    0    0    0    0    0    0    0   32    0   72    0
END

View in JSmol

Synonyms

Value	Source
Hollow cylinder protein complex	MeSH

Chemical Formula

C₃₁H₅₂O

Average Mass

440.7560 Da

Monoisotopic Mass

440.40182 Da

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

CO[C@H]1CC[C@@]2(C)[C@@H](CC[C@@H]3C2=CC[C@]2(C)[C@H]4CC[C@@H](C(C)C)[C@]4(C)CC[C@@]32C)C1(C)C

InChI Identifier

InChI=1S/C31H52O/c1-20(2)21-10-13-25-29(21,6)18-19-30(7)23-11-12-24-27(3,4)26(32-9)15-16-28(24,5)22(23)14-17-31(25,30)8/h14,20-21,23-26H,10-13,15-19H2,1-9H3/t21-,23+,24-,25-,26-,28+,29-,30-,31+/m0/s1

InChI Key

MRNPHCMRIQYRFU-UWAWSDATSA-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
Attalea cohune	LOTUS Database	35616633
Diospyros discolor	LOTUS Database	35616633
Diospyros nigra	LOTUS Database	35616633
Elaeis guineensis	LOTUS Database	35616633
Saccharum spontaneum	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Triterpenoids

Direct Parent

Triterpenoids

Alternative Parents

Substituents

Triterpenoid
Steroid
Delta-5-steroid
Ether
Dialkyl ether
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Aliphatic homopolycyclic compound

Molecular Framework

Aliphatic homopolycyclic compounds

External Descriptors

triterpenoid (CHEBI:81166 )

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

C00040278

Chemspider ID

164262

KEGG Compound ID

C17534

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

189045

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Liu X, Ganguly P, Jin Y, Jhatro MJ, Shea JE, Buratto SK, Bowers MT: Tachykinin Neuropeptides and Amyloid beta (25-35) Assembly: Friend or Foe? J Am Chem Soc. 2022 Aug 17;144(32):14614-14626. doi: 10.1021/jacs.2c03845. Epub 2022 Aug 2. [PubMed:35917596 ]
Sulatskaya AI, Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV: sfGFP throws light on the early stages of beta-barrel amyloidogenesis. Int J Biol Macromol. 2022 Aug 31;215:224-234. doi: 10.1016/j.ijbiomac.2022.06.108. Epub 2022 Jun 17. [PubMed:35718155 ]
Laos V, Bishop D, Ganguly P, Schonfeld G, Trapp E, Cantrell KL, Buratto SK, Shea JE, Bowers MT: Catalytic Cross Talk between Key Peptide Fragments That Couple Alzheimer's Disease with Amyotrophic Lateral Sclerosis. J Am Chem Soc. 2021 Mar 10;143(9):3494-3502. doi: 10.1021/jacs.0c12729. Epub 2021 Feb 23. [PubMed:33621087 ]
Aki K, Okamura E: Side-chain conformers to allow conversion from normal to isoaspartate in age-related proteins and peptides. Biochim Biophys Acta Proteins Proteom. 2020 Nov;1868(11):140483. doi: 10.1016/j.bbapap.2020.140483. Epub 2020 Jul 10. [PubMed:32659262 ]
He J, Deng Y, Zhu F, Zhong T, Luo N, Lei L, Cheng L, Hu T: The Efficacy and Safety of a Herbal Toothpaste in Reducing Gingivitis: A Double-Blind, Randomized, Placebo-Controlled, Parallel Allocation Clinical Trial. Evid Based Complement Alternat Med. 2019 Feb 3;2019:3764936. doi: 10.1155/2019/3764936. eCollection 2019. [PubMed:30854006 ]
LOTUS database [Link]

Showing NP-Card for cylindrin (NP0241176)

MOL for NP0241176 (cylindrin)

3D MOL for NP0241176 (cylindrin)

3D SDF for NP0241176 (cylindrin)

3D-SDF for NP0241176 (cylindrin)

PDB for NP0241176 (cylindrin)

3D PDB for NP0241176 (cylindrin)

SMILES for NP0241176 (cylindrin)

INCHI for NP0241176 (cylindrin)

Structure for NP0241176 (cylindrin)

3D Structure for NP0241176 (cylindrin)