4NJD | pdb_00004njd

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

• PDB DOI: https://doi.org/10.2210/pdb4NJD/pdb

• Classification: Transferase/Transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-09 Released: 2014-05-21 
• Deposition Author(s): Park, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.321 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.235 (Depositor) 
• R-Value Observed: 
  0.239 (Depositor) 

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

• PubMed: 24704155 
• DOI: https://doi.org/10.1016/j.canlet.2014.03.024
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Translational Therapeutics, Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Republic of Korea.
School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea.
Medicinal Chemistry Research Center, Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Republic of Korea.
Research Institute, DongWha Pharm. Co., Gyeonggi-do 446-902, Republic of Korea.
Laboratory of Translational Therapeutics, Korea Research Institute of Chemical Technology, Yuseong-Gu, Daejeon 305-600, Republic of Korea. Electronic address: [e-mail].
School of Systems Biomedical Science, Soongsil University, Seoul 156-743, Republic of Korea. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.83 kDa 
• Atom Count: 2,382 
• Modeled Residue Count: 291 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 4	A	296	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NJD	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
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
NJD	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 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.235 (Depositor) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.559	α = 90
b = 65.559	β = 90
c = 183.6	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references, Derived calculations
• Version 1.2: 2024-10-16
  Changes: Data collection, Structure summary