Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 33.04 kDa 
• Atom Count: 2322 
• Modelled Residue Count: 290 
• Deposited Residue Count: 290 
• Unique protein chains: 1

5XVF

Crystal Structure of PAK4 in complex with inhibitor CZH062

• DOI: 10.2210/pdb5XVF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.251 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

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

• PubMed: 29190083 
• DOI: 10.1021/acs.jmedchem.7b01342
• Primary Citation of Related Structures:  
  5XVA, 5XVF, 5XVG


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	A	290	Homo sapiens	Mutation(s): 0  Gene Names: PAK4, KIAA1142 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O96013 (Homo sapiens) Explore O96013  Go to UniProtKB:  O96013
PHAROS:  O96013 GTEx:  ENSG00000130669

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8FR (Subject of Investigation/LOI)	B [auth A]	2-(4-azanylpiperidin-1-yl)-6-chloranyl-N-(1-methylimidazol-4-yl)quinazolin-4-amine C17 H20 Cl N7 FFRWUFYTZPMLTK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
8FR	BindingDB:  5XVF	Ki: 710 (nM) from 1 assay(s)
		Kd: 156 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.251 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.404	α = 90
b = 65.404	β = 90
c = 180.863	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data collection
HKL-2000	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Ligand Structure Quality Assessment  

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