5IDP

CDK8-CYCC IN COMPLEX WITH (3-Amino-1H-indazol-5-yl)-[(S)-2-(4-fluoro-phenyl)-piperidin-1-yl]-methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report



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:  
    5IDN, 5ICP, 5IDP

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 8A370Homo sapiensMutation(s): 0 
Gene Names: CDK8
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
Find proteins for P49336 (Homo sapiens)
Explore P49336 
Go to UniProtKB:  P49336
NIH Common Fund Data Resources
PHAROS  P49336
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-CB268Homo sapiensMutation(s): 0 
Gene Names: CCNC
Find proteins for P24863 (Homo sapiens)
Explore P24863 
Go to UniProtKB:  P24863
NIH Common Fund Data Resources
PHAROS  P24863
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6A6
Query on 6A6

Download CCD File 
A
(3-amino-1H-indazol-5-yl)[(2S)-2-(4-fluorophenyl)piperidin-1-yl]methanone
C19 H19 F N4 O
VXYMGUGNDZARSZ-KRWDZBQOSA-N
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6A6IC50:  45   nM  BindingDB
6A6IC50:  800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.113α = 90
b = 71.093β = 90
c = 172.335γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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