9D1X | pdb_00009d1x

Crystal structure of FGFR3 bound to indazole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb9D1X/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2024-08-08 Released: 2025-06-25 
• Deposition Author(s): Postel, S., Johnson, Z.L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.190 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

OPLS5: Addition of Polarizability and Improved Treatment of Metals

Damm, W., Dajnowicz, S., Ghoreishi, D., Yu, Y., Ganeshan, K., Madin, O., Rudshteyn, B., Hu, R., Wu, M., Shang, Y., Albanese, S., Zou, Y., Ye, M., Johnson, Z., Trzoss, M., Rafi, S., Kapilashrami, K., Saleh, N., Ghanakota, P., Zhang, Y., Sampson, J., Chen, W., Wang, L., Dahlgren, M., Russell, E., Leffler, A., Abel, R., Friesner, R., Harder, E.

(2024) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2024-2svr7

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.18 kDa 
• Atom Count: 2,519 
• Modeled Residue Count: 282 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 3	A	297	Homo sapiens	Mutation(s): 2  Gene Names: FGFR3, JTK4 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P22607 (Homo sapiens) Explore P22607  Go to UniProtKB:  P22607
PHAROS:  P22607 GTEx:  ENSG00000068078

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A6M (Subject of Investigation/LOI)	B [auth A]	(3P)-N-(2,6-dimethylphenyl)-6-methoxy-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazole-5-carboxamide C21 H21 N5 O2 FPFXIZOOXNNWKA-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.190 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.191 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.87	α = 90
b = 55.87	β = 90
c = 365.784	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Postel, S., Johnson, Z.L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release