8S15 | pdb_00008s15

c-KIT kinase domain in complex with nintedanib

• PDB DOI: https://doi.org/10.2210/pdb8S15/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., Kleinboelting, S.B., 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: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

c-KIT kinase domain in complex with nintedanib

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.73 kDa 
• Atom Count: 2,555 
• Modeled Residue Count: 312 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mast/stem cell growth factor receptor Kit	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XIN (Subject of Investigation/LOI)	B [auth A]	methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate C31 H33 N5 O4 XZXHXSATPCNXJR-ZIADKAODSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.35	α = 90
b = 54.35	β = 90
c = 456.07	γ = 120

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., Kleinboelting, S.B., 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