4ZJI

PAK1 in complex with 2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Optimization of a Dibenzodiazepine Hit to a Potent and Selective Allosteric PAK1 Inhibitor.

Karpov, A.S.Amiri, P.Bellamacina, C.Bellance, M.H.Breitenstein, W.Daniel, D.Denay, R.Fabbro, D.Fernandez, C.Galuba, I.Guerro-Lagasse, S.Gutmann, S.Hinh, L.Jahnke, W.Klopp, J.Lai, A.Lindvall, M.K.Ma, S.Mobitz, H.Pecchi, S.Rummel, G.Shoemaker, K.Trappe, J.Voliva, C.Cowan-Jacob, S.W.Marzinzik, A.L.

(2015) Acs Med.Chem.Lett. 6: 776-781

  • DOI: 10.1021/acsmedchemlett.5b00102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of inhibitors targeting novel allosteric kinase sites is very challenging. Such compounds, however, once identified could offer exquisite levels of selectivity across the kinome. Herein we report our structure-based optimization strateg ...

    The discovery of inhibitors targeting novel allosteric kinase sites is very challenging. Such compounds, however, once identified could offer exquisite levels of selectivity across the kinome. Herein we report our structure-based optimization strategy of a dibenzodiazepine hit 1, discovered in a fragment-based screen, yielding highly potent and selective inhibitors of PAK1 such as 2 and 3. Compound 2 was cocrystallized with PAK1 to confirm binding to an allosteric site and to reveal novel key interactions. Compound 3 modulated PAK1 at the cellular level and due to its selectivity enabled valuable research to interrogate biological functions of the PAK1 kinase.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research , Novartis Campus, CH-4056 Basel, Switzerland.,Novartis Institutes for BioMedical Research , 5300 Chiron Way, Emeryville, California 94608, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 1
A, B, C, D
299Homo sapiensMutation(s): 0 
Gene Names: PAK1
EC: 2.7.11.1
Find proteins for Q13153 (Homo sapiens)
Go to Gene View: PAK1
Go to UniProtKB:  Q13153
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4OQ
Query on 4OQ

Download SDF File 
Download CCD File 
A, B, C, D
2-chloro-5-ethyl-8-fluoro-11-(4-methylpiperazin-1-yl)-dibenzodiazepine
C20 H22 Cl F N4
NQBRFDSRSGHBBK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4OQIC50: 323 nM (100) BINDINGDB
4OQKd: 340 - >40000 nM (100) BINDINGDB
4OQKd: 340 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 110.520α = 90.00
b = 115.060β = 90.00
c = 116.360γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-29
    Type: Database references