PAK1 in complex with (S)-N-(tert-butyl)-3-((2-chloro-5-ethyl-8-fluoro-dibenzodiazepin-11-yl)amino)pyrrolidine-1-carboxamide

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1021/acsmedchemlett.5b00102
  • Primary Citation of Related Structures:  
    4ZJI, 4ZJJ, 4ZLO

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 1
A, B, C, D
299Homo sapiensMutation(s): 0 
Gene Names: PAK1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens)
Explore Q13153 
Go to UniProtKB:  Q13153
PHAROS:  Q13153
GTEx:  ENSG00000149269 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13153
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
4OR BindingDB:  4ZJJ Kd: min: 9.9, max: 4.00e+4 (nM) from 3 assay(s)
IC50: 18 (nM) from 1 assay(s)
Binding MOAD:  4ZJJ Kd: 9.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.33α = 90
b = 113.79β = 90
c = 116.36γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations