8S17 | pdb_00008s17

c-KIT kinase domain in complex with ponatinib

• PDB DOI: https://doi.org/10.2210/pdb8S17/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-02-15 Released: 2025-09-03 
• Deposition Author(s): Teuber, A., Mueller, M.P., Rauh, D.
• Funding Organization(s): German Research Foundation (DFG), European Regional Development Fund, German Federal Ministry for Education and Research, Other government, Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

c-KIT kinase domain in complex with ponatinib

Teuber, A., Niggenaber, J., Kleinboelting, S.B., Landel, I., Warmuth, J., Busick, D., Mueller, M.P., Bauer, S., Rauh, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 75.6 kDa 
• Atom Count: 4,904 
• Modeled Residue Count: 589 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor Kit	A, B	327	Homo sapiens	Mutation(s): 14  Gene Names: KIT, SCFR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P10721 (Homo sapiens) Explore P10721  Go to UniProtKB:  P10721
PHAROS:  P10721 GTEx:  ENSG00000157404

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0LI (Subject of Investigation/LOI)	C [auth A], H [auth B]	3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide C29 H27 F3 N6 O PHXJVRSECIGDHY-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.01	α = 90
b = 90.61	β = 90
c = 91.41	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Teuber, A., Mueller, M.P., Rauh, D.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	RA 1055/3-2
European Regional Development Fund	European Union	EFRE-800400
German Federal Ministry for Education and Research	Germany	01ZX2201B
Other government		NW21-062C
Other private		Ex-2021-0033

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release