5XVA

Crystal Structure of PAK4 in complex with inhibitor CZH216


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.847 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure-Based Design of 6-Chloro-4-aminoquinazoline-2-carboxamide Derivatives as Potent and Selective p21-Activated Kinase 4 (PAK4) Inhibitors.

Hao, C.Zhao, F.Song, H.Guo, J.Li, X.Jiang, X.Huan, R.Song, S.Zhang, Q.Wang, R.Wang, K.Pang, Y.Liu, T.Lu, T.Huang, W.Wang, J.Lin, B.He, Z.Li, H.Li, F.Zhao, D.Cheng, M.

(2018) J. Med. Chem. 61: 265-285

  • DOI: 10.1021/acs.jmedchem.7b01342
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Herein, we report the discovery and characterization of a novel class of PAK4 inhibitors with a quinazoline scaffold. Based on the shape and chemical composition of the ATP-binding pocket of PAKs, we chose a 2,4-diaminoquinazoline series of inhibitor ...

    Herein, we report the discovery and characterization of a novel class of PAK4 inhibitors with a quinazoline scaffold. Based on the shape and chemical composition of the ATP-binding pocket of PAKs, we chose a 2,4-diaminoquinazoline series of inhibitors as a starting point. Guided by X-ray crystallography and a structure-based drug design (SBDD) approach, a series of novel 4-aminoquinazoline-2-carboxamide PAK4 inhibitors were designed and synthesized. The inhibitors' selectivity, therapeutic potency, and pharmaceutical properties were optimized. One of the best compounds, 31 (CZh226), showed remarkable PAK4 selectivity (346-fold vs PAK1) and favorable kinase selectivity profile. Moreover, this compound potently inhibited the migration and invasion of A549 tumor cells by regulating the PAK4-directed downstream signaling pathways in vitro. Taken together, these data support the further development of 31 as a lead compound for PAK4-targeted anticancer drug discovery and as a valuable research probe for the further biological investigation of group II PAKs.


    Organizational Affiliation

    Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase PAK 4
A
293Homo sapiensMutation(s): 0 
Gene Names: PAK4 (KIAA1142)
EC: 2.7.11.1
Find proteins for O96013 (Homo sapiens)
Go to Gene View: PAK4
Go to UniProtKB:  O96013
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8FU
Query on 8FU

Download SDF File 
Download CCD File 
A
[6-chloranyl-4-[(5-methyl-1H-pyrazol-3-yl)amino]quinazolin-2-yl]-[(3R)-3-methylpiperazin-1-yl]methanone
C18 H20 Cl N7 O
WQTMYTFWTYPJST-LLVKDONJSA-N
 Ligand Interaction
EOH
Query on EOH

Download SDF File 
Download CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.847 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.649α = 90.00
b = 64.699β = 90.00
c = 100.000γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-06-27 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Zhao, F., Li, H.

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release