9U3N | pdb_00009u3n

Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-01

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2025-03-18 Released: 2025-04-23 
  • Deposition Author(s): Chen, L.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.342 (Depositor), 0.340 (DCC) 
  • R-Value Work: 
    0.279 (Depositor), 0.283 (DCC) 

Starting Model: experimental
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Literature

Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with compound LC-F2-1

Chen, L.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor receptor 2
A, B
311Homo sapiensMutation(s): 1 
Gene Names: FGFR2, BEK, KGFR, KSAM
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens)
Explore P21802 
Go to UniProtKB:  P21802
PHAROS:  P21802
GTEx:  ENSG00000066468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21802
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ENT (Subject of Investigation/LOI)
Query on A1ENT
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		~{N}-[4-[4-azanyl-7-methyl-5-[2-(3-methylimidazo[4,5-b]pyridin-6-yl)ethynyl]pyrrolo[2,3-d]pyrimidin-6-yl]phenyl]prop-2-enamide
C25 H20 N8 O
DICKGCNITDYTHW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free:  0.342 (Depositor), 0.340 (DCC) 
  • R-Value Work:  0.279 (Depositor), 0.283 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.069α = 90
b = 88.713β = 90
c = 127.42γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-04-23 
    • Deposition Author(s): Chen, L.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82422068

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release