Crystal structure of P21-activated kinase 1 (PAK1) in complex with compound 9

Experimental Data Snapshot

  • Resolution: 2.22 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Chemically Diverse Group I p21-Activated Kinase (PAK) Inhibitors Impart Acute Cardiovascular Toxicity with a Narrow Therapeutic Window.

Rudolph, J.Murray, L.J.Ndubaku, C.O.O'Brien, T.Blackwood, E.Wang, W.Aliagas, I.Gazzard, L.Crawford, J.J.Drobnick, J.Lee, W.Zhao, X.Hoeflich, K.P.Favor, D.A.Dong, P.Zhang, H.Heise, C.E.Oh, A.Ong, C.C.La, H.Chakravarty, P.Chan, C.Jakubiak, D.Epler, J.Ramaswamy, S.Vega, R.Cain, G.Diaz, D.Zhong, Y.

(2016) J Med Chem 59: 5520-5541

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00638
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    p21-activated kinase 1 (PAK1) has an important role in transducing signals in several oncogenic pathways. The concept of inhibiting this kinase has garnered significant interest over the past decade, particularly for targeting cancers associated with PAK1 amplification. Animal studies with the selective group I PAK (pan-PAK1, 2, 3) inhibitor G-5555 from the pyrido[2,3-d]pyrimidin-7-one class uncovered acute toxicity with a narrow therapeutic window. To attempt mitigating the toxicity, we introduced significant structural changes, culminating in the discovery of the potent pyridone side chain analogue G-9791. Mouse tolerability studies with this compound, other members of this series, and compounds from two structurally distinct classes revealed persistent toxicity and a correlation of minimum toxic concentrations and PAK1/2 mediated cellular potencies. Broad screening of selected PAK inhibitors revealed PAK1, 2, and 3 as the only overlapping targets. Our data suggest acute cardiovascular toxicity resulting from the inhibition of PAK2, which may be enhanced by PAK1 inhibition, and cautions against continued pursuit of pan-group I PAK inhibitors in drug discovery.

  • Organizational Affiliation

    Shanghai Chempartner Inc. , 998 Halei Road, Zhangjiang Hi-Tech Park, Pudong New Area, Shanghai 201203, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 1
A, B
300Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13153
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6BZ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C22 H22 Cl N7 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
6BZ Binding MOAD:  5IME Ki: 4.6 (nM) from 1 assay(s)
BindingDB:  5IME Ki: 4.6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.22 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.48α = 90
b = 82.82β = 106.71
c = 65.89γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata 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: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description