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 

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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 

  • DOI: 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 ...

    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: 

    School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea. Electronic address: psy@ssu.ac.kr.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4A296Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NJD (Subject of Investigation/LOI)
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		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		AL-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

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Ligand Structure Quality Assessment  


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Entry History 

Deposition Data

  • Deposited Date: 2013-11-09 
  • 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