4NJD

Structure of p21-activated kinase 4 with a novel inhibitor KY-04031


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery and the structural basis of a novel p21-activated kinase 4 inhibitor.

Ryu, B.J.Kim, S.Min, B.Kim, K.Y.Lee, J.S.Park, W.J.Lee, H.Kim, S.H.Park, S.

(2014) Cancer Lett 349: 45-50

  • DOI: https://doi.org/10.1016/j.canlet.2014.03.024
  • Primary Citation of Related Structures:  
    4NJD

  • PubMed Abstract: 

    Functional versatility and elevated expression in cancers have endowed p21-activated kinase 4 (PAK4) as one of the first-in-class anti-cancer drug target. In this study, a novel PAK4 inhibitor, KY-04031 (N(2)-(2-(1H-indol-3-yl)ethyl)-N(4)-(1H-indazol-5-yl)-6-methoxy-1,3,5-triazine-2,4-diamine), was discovered using a high-throughput screening. Analysis of the complex crystal structure illustrated that both indole and indazole of KY-04031 are responsible for PAK4 hinge interaction. Moreover, the molecule's triazine core was found to mimic the ribose of the natural ATP substrate. The cell-based anti-cancer potency of KY-04031 was less effective than the pyrroloaminopyrazoles; however, the unique molecular feature of KY-04031 can be exploited in designing new PAK4 inhibitors.


  • Organizational Affiliation

    Laboratory of Translational Therapeutics, Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4296Homo sapiensMutation(s): 0 
Gene Names: PAK4
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96013
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NJD
Query on NJD

Download Ideal Coordinates CCD File 
B [auth A]N-(1H-indazol-5-yl)-N'-[2-(1H-indol-3-yl)ethyl]-6-methoxy-1,3,5-triazine-2,4-diamine
C21 H20 N8 O
NSJQROISOSHTBB-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
NJD Binding MOAD:  4NJD IC50: 790 (nM) from 1 assay(s)
BindingDB:  4NJD IC50: 790 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.321 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.559α = 90
b = 65.559β = 90
c = 183.6γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-05-21 
  • Deposition Author(s): Park, S.

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations