5HBJ

CDK8-CYCC IN COMPLEX WITH 8-[2-Amino-3-chloro-5-(1-methyl-1H-indazol-5-yl)-pyridin-4-yl]-2,8-diaza-spiro[4.5]decan-1-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19.

Mallinger, A.Schiemann, K.Rink, C.Stieber, F.Calderini, M.Crumpler, S.Stubbs, M.Adeniji-Popoola, O.Poeschke, O.Busch, M.Czodrowski, P.Musil, D.Schwarz, D.Ortiz-Ruiz, M.J.Schneider, R.Thai, C.Valenti, M.de Haven Brandon, A.Burke, R.Workman, P.Dale, T.Wienke, D.Clarke, P.A.Esdar, C.Raynaud, F.I.Eccles, S.A.Rohdich, F.Blagg, J.

(2016) J.Med.Chem. 59: 1078-1101

  • DOI: 10.1021/acs.jmedchem.5b01685
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Mediator complex-associated cyclin-dependent kinase CDK8 has been implicated in human disease, particularly in colorectal cancer where it has been reported as a putative oncogene. Here we report the discovery of 109 (CCT251921), a potent, selecti ...

    The Mediator complex-associated cyclin-dependent kinase CDK8 has been implicated in human disease, particularly in colorectal cancer where it has been reported as a putative oncogene. Here we report the discovery of 109 (CCT251921), a potent, selective, and orally bioavailable inhibitor of CDK8 with equipotent affinity for CDK19. We describe a structure-based design approach leading to the discovery of a 3,4,5-trisubstituted-2-aminopyridine series and present the application of physicochemical property analyses to successfully reduce in vivo metabolic clearance, minimize transporter-mediated biliary elimination while maintaining acceptable aqueous solubility. Compound 109 affords the optimal compromise of in vitro biochemical, pharmacokinetic, and physicochemical properties and is suitable for progression to animal models of cancer.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London, SW7 3RP, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 8
A
364Homo 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
270Homo 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 
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
5Y8
Query on 5Y8

Download SDF File 
Download CCD File 
A
8-[2-azanyl-3-chloranyl-5-(1-methylindazol-5-yl)pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one
C21 H23 Cl N6 O
VPJXPDLMACOGIZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5Y8IC50: 2.3 - 4.9 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.288 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.749α = 90.00
b = 71.774β = 90.00
c = 176.434γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Database references