5IDN

CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)-methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening.

Czodrowski, P.Mallinger, A.Wienke, D.Esdar, C.Poschke, O.Busch, M.Rohdich, F.Eccles, S.A.Ortiz-Ruiz, M.J.Schneider, R.Raynaud, F.I.Clarke, P.A.Musil, D.Schwarz, D.Dale, T.Urbahns, K.Blagg, J.Schiemann, K.

(2016) J. Med. Chem. 59: 9337-9349

  • DOI: 10.1021/acs.jmedchem.6b00597
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mediator complex-associated cyclin dependent kinase CDK8 regulates β-catenin-dependent transcription following activation of WNT signaling. Multiple lines of evidence suggest CDK8 may act as an oncogene in the development of colorectal cancer. He ...

    The mediator complex-associated cyclin dependent kinase CDK8 regulates β-catenin-dependent transcription following activation of WNT signaling. Multiple lines of evidence suggest CDK8 may act as an oncogene in the development of colorectal cancer. Here we describe the successful optimization of an imidazo-thiadiazole series of CDK8 inhibitors that was identified in a high-throughput screening campaign and further progressed by structure-based design. In several optimization cycles, we improved the microsomal stability, potency, and kinase selectivity. The initial imidazo-thiadiazole scaffold was replaced by a 3-methyl-1H-pyrazolo[3,4-b]-pyridine which resulted in compound 25 (MSC2530818) that displayed excellent kinase selectivity, biochemical and cellular potency, microsomal stability, and is orally bioavailable. Furthermore, we demonstrated modulation of phospho-STAT1, a pharmacodynamic biomarker of CDK8 activity, and tumor growth inhibition in an APC mutant SW620 human colorectal carcinoma xenograft model after oral administration. Compound 25 demonstrated suitable potency and selectivity to progress into preclinical in vivo efficacy and safety studies.


    Organizational Affiliation

    Merck KGaA , Frankfurter Strasse 250, Darmstadt, 64293, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 8
A
370Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.22, 2.7.11.23
Find proteins for P49336 (Homo sapiens)
Go to Gene View: CDK8
Go to UniProtKB:  P49336
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-C
B
267Homo sapiensMutation(s): 0 
Gene Names: CCNC
Find proteins for P24863 (Homo sapiens)
Go to Gene View: CCNC
Go to UniProtKB:  P24863
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
6A7
Query on 6A7

Download SDF File 
Download CCD File 
A
[(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone
C18 H17 Cl N4 O
ODRITQGYYWHQGM-INIZCTEOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.460α = 90.00
b = 73.467β = 90.00
c = 168.020γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release