8S1A | pdb_00008s1a

c-KIT kinase domain in complex with crenolanib

  • 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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.208 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 

Literature

c-KIT kinase domain in complex with crenolanib

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

To be published.

Macromolecule Content 

  • Total Structure Weight: 75.28 kDa 
  • Atom Count: 5,260 
  • Modeled Residue Count: 593 
  • Deposited Residue Count: 654 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mast/stem cell growth factor receptor Kit
A, B
327Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10721
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6T2
(Subject of Investigation/LOI)

Query on 6T2


Download:Ideal Coordinates CCD File
C [auth A],
D [auth B]		1-(2-{5-[(3-Methyloxetan-3-yl)methoxy]-1H-benzimidazol-1-yl}quinolin-8-yl)piperidin-4-amine
C26 H29 N5 O2
DYNHJHQFHQTFTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.208 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.54α = 90
b = 59.53β = 90
c = 191.41γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyRA 1055/3-2
European Regional Development FundEuropean UnionEFRE-800400
German Federal Ministry for Education and ResearchGermany01ZX2201B
Other governmentNW21-062C
Other privateEx-2021-0033

Revision History  (Full details and data files)

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