2HXL

crystal structure of Chek1 in complex with inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of 6-substituted indolylquinolinones as potent Chek1 kinase inhibitors.

Huang, S.Garbaccio, R.M.Fraley, M.E.Steen, J.Kreatsoulas, C.Hartman, G.Stirdivant, S.Drakas, B.Rickert, K.Walsh, E.Hamilton, K.Buser, C.A.Hardwick, J.Mao, X.Abrams, M.Beck, S.Tao, W.Lobell, R.Sepp-Lorenzino, L.Yan, Y.Ikuta, M.Murphy, J.Z.Sardana, V.Munshi, S.Kuo, L.Reilly, M.Mahan, E.

(2006) Bioorg.Med.Chem.Lett. 16: 5907-5912

  • DOI: 10.1016/j.bmcl.2006.08.053
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Through a comparison of X-ray co-crystallographic data for 1 and 2 in the Chek1 active site, it was hypothesized that the affinity of the indolylquinolinone series (2) for Chek1 kinase would be improved via C6 substitution into the hydrophobic region ...

    Through a comparison of X-ray co-crystallographic data for 1 and 2 in the Chek1 active site, it was hypothesized that the affinity of the indolylquinolinone series (2) for Chek1 kinase would be improved via C6 substitution into the hydrophobic region I (HI) pocket. An efficient route to 6-bromo-3-indolyl-quinolinone (9) was developed, and this series was rapidly optimized for potency by modification at C6. A general trend was observed among these low nanomolar Chek1 inhibitors that compounds with multiple basic amines, or elevated polar surface area (PSA) exhibited poor cell potency. Minimization of these parameters (basic amines, PSA) resulted in Chek1 inhibitors with improved cell potency, and preliminary pharmacokinetic data are presented for several of these compounds.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. shaei_huang@merck.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase Chk1
A
322Homo sapiensMutation(s): 0 
Gene Names: CHEK1 (CHK1)
EC: 2.7.11.1
Find proteins for O14757 (Homo sapiens)
Go to Gene View: CHEK1
Go to UniProtKB:  O14757
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
422
Query on 422

Download SDF File 
Download CCD File 
A
3-(5-{[4-(AMINOMETHYL)PIPERIDIN-1-YL]METHYL}-1H-INDOL-2-YL)-1H-INDAZOLE-6-CARBONITRILE
C23 H24 N6
WBKUBPBCFYCSRT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
422IC50: 12 nM (100) BINDINGDB
422IC50: 12 nM BINDINGMOAD
422IC50: 12 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.100α = 90.00
b = 65.640β = 94.82
c = 58.140γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
CNSphasing
CrystalCleardata collection
d*TREKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-08-03 
  • Released Date: 2007-06-19 
  • Deposition Author(s): Yan, Y.

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance