4IQ6

Gsk-3beta with inhibitor 6-chloro-N-cyclohexyl-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Azaindole-Based Inhibitors of Cdc7 Kinase: Impact of the Pre-DFG Residue, Val 195.

Tong, Y.Stewart, K.D.Florjancic, A.S.Harlan, J.E.Merta, P.J.Przytulinska, M.Soni, N.Swinger, K.K.Zhu, H.Johnson, E.F.Shoemaker, A.R.Penning, T.D.

(2013) ACS Med Chem Lett 4: 211-215

  • DOI: 10.1021/ml300348c

  • PubMed Abstract: 
  • To investigate the role played by the unique pre-DFG residue Val 195 of Cdc7 kinase on the potency of azaindole-chloropyridines (1), a series of novel analogues with various chloro replacements were synthesized and evaluated for their inhibitory acti ...

    To investigate the role played by the unique pre-DFG residue Val 195 of Cdc7 kinase on the potency of azaindole-chloropyridines (1), a series of novel analogues with various chloro replacements were synthesized and evaluated for their inhibitory activity against Cdc7. X-ray cocrystallization using a surrogate protein, GSK3β, and modeling studies confirmed the azaindole motif as the hinge binder. Weaker hydrophobic interactions with Met 134 and Val 195 by certain chloro replacements (e.g., H, methyl) led to reduced Cdc7 inhibition. Meanwhile, data from other replacements (e.g., F, O) indicated that loss of such hydrophobic interaction could be compensated by enhanced hydrogen bonding to Lys 90. Our findings not only provide an in-depth understanding of the pre-DFG residue as another viable position impacting kinase inhibition, they also expand the existing knowledge of ligand-Cdc7 binding.


    Organizational Affiliation

    Cancer Research, Structural Biology, Lead Discovery, and Protein Biochemistry, Global Pharmaceutical Research and Development, Abbott Laboratories , 100 Abbott Park Road, Abbott Park, Illinois 60064, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen synthase kinase-3 beta
A, B
426Homo sapiensGene Names: GSK3B
EC: 2.7.11.1, 2.7.11.26
Find proteins for P49841 (Homo sapiens)
Go to Gene View: GSK3B
Go to UniProtKB:  P49841
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IQ6
Query on IQ6

Download SDF File 
Download CCD File 
A, B
6-chloro-N-cyclohexyl-4-(1H-pyrrolo[2,3-b]pyridin-3-yl)pyridin-2-amine
C18 H19 Cl N4
JKTMEYXRCJFWAI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IQ6Ki: 58 nM (100) BINDINGDB
IQ6Ki: 58 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.12 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.835α = 90.00
b = 84.991β = 90.00
c = 178.058γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
MOLREPphasing
JDirectordata collection
XDSdata reduction
AutoPROCdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-24
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description