9WDD | pdb_00009wdd

Crystal structure of NAMPT-KPT-7523 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.194 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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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: 112.23 kDa 
  • Atom Count: 8,685 
  • Modeled Residue Count: 938 
  • Deposited Residue Count: 982 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nicotinamide phosphoribosyltransferase
A, B
491Homo sapiensMutation(s): 0 
Gene Names: NAMPTPBEFPBEF1
EC: 2.4.2.12
UniProt & NIH Common Fund Data Resources
Find proteins for P43490 (Homo sapiens)
Explore P43490 
Go to UniProtKB:  P43490
PHAROS:  P43490
GTEx:  ENSG00000105835 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43490
Sequence Annotations
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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
C [auth A],
D [auth B]
(~{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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.194 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.837α = 90
b = 107.229β = 96.83
c = 83.386γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
PHENIXmodel building

Structure Validation

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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