6TPA

CDK8/CyclinC in complex with drug ETP-50775


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Pyrido[2,3-b][1,5]benzoxazepin-5(6H)-one derivatives as CDK8 inhibitors.

Martinez-Gonzalez, S.Garcia, A.B.Albarran, M.I.Cebria, A.Amezquita-Alves, A.Garcia-Campos, F.J.Martinez-Gago, J.Martinez-Torrecuadrada, J.Munoz, I.Blanco-Aparicio, C.Pastor, J.

(2020) Eur J Med Chem 201: 112443-112443

  • DOI: 10.1016/j.ejmech.2020.112443
  • Primary Citation of Related Structures:  
    6TPA

  • PubMed Abstract: 
  • CDK8 is a cyclin-dependent kinase that forms part of the mediator complex, and modulates the transcriptional output from distinct transcription factors involved in oncogenic control. Overexpression of CDK8 has been observed in various cancers, representing a potential target for developing novel CDK8 inhibitors in cancer therapeutics ...

    CDK8 is a cyclin-dependent kinase that forms part of the mediator complex, and modulates the transcriptional output from distinct transcription factors involved in oncogenic control. Overexpression of CDK8 has been observed in various cancers, representing a potential target for developing novel CDK8 inhibitors in cancer therapeutics. In the course of our investigations to discover new CDK8 inhibitors, we designed and synthesized tricyclic pyrido[2,3-b][1,5]benzoxazepin-5(6H)-one derivatives, by introduction of chemical complexity in the multi-kinase inhibitor Sorafenib taking into account the flexibility of the P-loop motif of CDK8 protein observed after analysis of structural information of co-crystallized CDK8 inhibitors. In vitro evaluation of the inhibitory activity of the prepared compounds against CDK8 led us to identify compound 2 as the most potent inhibitor of the series (IC 50  = 8.25 nM). Co-crystal studies and the remarkable selectivity profile of compound 2 are presented. Compound 2 showed moderate reduction of phosphorylation of CDK8 substrate STAT1 in cells, in line with other reported Type II CDK8 inhibitors. We propose herein an alternative to find a potential therapeutic use for this chemical series.


    Organizational Affiliation

    Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), C/ Melchor Fernández Almagro 3, E-28029, Madrid, Spain. Electronic address: jpastor@cnio.es.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 8A405Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49336 (Homo sapiens)
Explore P49336 
Go to UniProtKB:  P49336
PHAROS:  P49336
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-CB285Homo sapiensMutation(s): 0 
Gene Names: CCNC
UniProt & NIH Common Fund Data Resources
Find proteins for P24863 (Homo sapiens)
Explore P24863 
Go to UniProtKB:  P24863
PHAROS:  P24863
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NZ8 (Subject of Investigation/LOI)
Query on NZ8

Download Ideal Coordinates CCD File 
C [auth A]1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-(5-oxidanylidene-6-pyridin-4-yl-pyrido[2,3-b][1,5]benzoxazepin-9-yl)urea
C25 H15 Cl F3 N5 O3
NQHGDUGVQSAKOR-UHFFFAOYSA-N
 Ligand Interaction
NZ5
Query on NZ5

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], S [auth B](2~{R})-butane-1,2-diol
C4 H10 O2
BMRWNKZVCUKKSR-SCSAIBSYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
D [auth A] , E [auth A] , F [auth A] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , N [auth B] , 
D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.985α = 90
b = 72.339β = 90
c = 189.127γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release