9WDF | pdb_00009wdf

Crystal structure of PAK4-KPT-7523 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.255 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.222 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9WDF

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Literature

Structural basis for a p21-activated kinase 4 and nicotinamide phosphoribosyltransferase dual inhibitor.

Park, J.Hong, H.R.Han, S.H.Song, J.Son, S.Y.Choi, S.Park, S.M.Lee, W.K.Jiko, C.Kim, J.H.Jee, J.G.Bang, J.K.Park, I.Y.Lee, S.J.

(2026) Acta Crystallogr D Struct Biol 

  • DOI: https://doi.org/10.1107/S2059798326006145
  • Primary Citation Related Structures: 
    9WDD, 9WDF

  • PubMed Abstract: 

    Simultaneous inhibition of oncogenic signaling and metabolic pathways represents a promising approach for cancer therapy. KPT-9274, a clinical stage compound, has been reported as a dual inhibitor of p21-activated kinase 4 (PAK4) and nicotinamide phosphoribosyltransferase (NAMPT), but its structural basis has remained undefined. Here, we present high-resolution crystal structures of PAK4 and NAMPT in complex with KPT-7523, an analog of KPT-9274, determined at 2.20 and 1.45 Å resolution, respectively. In PAK4, the 2-aminopyridine moiety of KPT-7523 enables dual binding, occupying the adenine-binding site for ATP and simultaneously engaging the substrate-binding cleft in the C-lobe, thereby interfering with both catalytic and regulatory functions. In NAMPT, the same scaffold inserts into the NAD + active site in an extended conformation that preserves critical interactions. Biophysical assays revealed distinct affinities across the two targets. These findings highlight the 2-aminopyridine moiety as a versatile pharmacophore that is adaptable to structurally unrelated proteins and provide a framework for designing next-generation dual inhibitors in cancer therapy.


  • Organizational Affiliation
    • College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea.

Macromolecule Content 

  • Total Structure Weight: 408.57 kDa 
  • Atom Count: 28,560 
  • Modeled Residue Count: 3,466 
  • Deposited Residue Count: 3,504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 4
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
292Homo 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
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
A1MBG
(Subject of Investigation/LOI)

Query on A1MBG



Download:Ideal Coordinates CCD File
AA [auth H]
BA [auth I]
CA [auth I]
DA [auth I]
EA [auth J]
AA [auth H],
BA [auth I],
CA [auth I],
DA [auth I],
EA [auth J],
FA [auth K],
GA [auth K],
HA [auth L],
IA [auth L],
JA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth E],
V [auth F],
W [auth F],
X [auth G],
Y [auth G],
Z [auth H]
(~{E})-3-(6-azanylpyridin-3-yl)-~{N}-[[(2~{S})-7-chloranyl-5-(4-piperazin-1-ylcarbonylphenyl)-2,3-dihydro-1-benzofuran-2-yl]methyl]prop-2-enamide
C28 H28 Cl N5 O3
VDACSASREQBHAZ-AJYURUAUSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.255 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.222 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.513α = 90
b = 208.671β = 103.34
c = 132.489γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
PHENIXmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release