5I0B

Structure of PAK4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


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Literature

The discovery and the structural basis of an imidazo[4,5-b]pyridine-based p21-activated kinase 4 inhibitor

Park, J.K.Kim, S.Han, Y.J.Kim, S.H.Kang, N.S.Lee, H.Park, S.Y.

(2016) Bioorg Med Chem Lett 26: 2580-2583

  • DOI: 10.1016/j.bmcl.2016.04.037
  • Primary Citation of Related Structures:  
    5I0B

  • PubMed Abstract: 
  • p21-Activated kinases (PAKs) which belong to the family of ste20 serine/threonine protein kinases regulate cytoskeletal reorganization, cell motility, cell proliferation, and oncogenic transformation which are all related to the cellular functions during cancer induction and metastasis ...

    p21-Activated kinases (PAKs) which belong to the family of ste20 serine/threonine protein kinases regulate cytoskeletal reorganization, cell motility, cell proliferation, and oncogenic transformation which are all related to the cellular functions during cancer induction and metastasis. The fact that PAK mutations are detected in multiple tumor tissues makes PAKs a novel therapeutic drug target. In this study, an imidazo[4,5-b]pyridine-based PAK4 inhibitor, KY-04045 (6-Bromo-2-(3-isopropyl-1-methyl-1H-pyrazol-4-yl)-1H-imidazo[4,5-b]pyridine), was discovered using a virtual site-directed fragment-based drug design and was validated using an inhibition assay. Although PAK4 affinity to KY-04045 seems much weaker than that of the reported PAK4 inhibitors, the location of KY-04045 is clearly defined in the structure of PAK4 co-crystallized with KY-04045. The crystal structure illustrates that the pyrazole and imidazopyridine rings of KY-04045 are sufficient for mediating PAK4 hinge loop interaction. Hence, we believe that KY-04045 can be exploited as a basic building block in designing novel imidazo[4,5-b]pyridine-based PAK4 inhibitors.


    Organizational Affiliation

    School of Systems Biomedical Science, Soongsil University, Seoul 06978, 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: PAK4KIAA1142
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
67U (Subject of Investigation/LOI)
Query on 67U

Download Ideal Coordinates CCD File 
B [auth A]6-bromo-2-[1-methyl-3-(propan-2-yl)-1H-pyrazol-4-yl]-1H-imidazo[4,5-b]pyridine
C13 H14 Br N5
XYHWYOLLASBNRO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.986α = 90
b = 62.986β = 90
c = 187.111γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-02-03 
  • Released Date: 2016-12-14 
  • Deposition Author(s): Park, S.Y.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic Of2013R1A1A2005276

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-14
    Type: Initial release