4U0I

Crystal structure of KIT in complex with ponatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Ponatinib Inhibits Polyclonal Drug-Resistant KIT Oncoproteins and Shows Therapeutic Potential in Heavily Pretreated Gastrointestinal Stromal Tumor (GIST) Patients.

Garner, A.P.Gozgit, J.M.Anjum, R.Vodala, S.Schrock, A.Zhou, T.Serrano, C.Eilers, G.Zhu, M.Ketzer, J.Wardwell, S.Ning, Y.Song, Y.Kohlmann, A.Wang, F.Clackson, T.Heinrich, M.C.Fletcher, J.A.Bauer, S.Rivera, V.M.

(2014) Clin.Cancer Res. 20: 5745-5755


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Mast/stem cell growth factor receptor Kit,Mast/stem cell growth factor receptor Kit
A
315Homo sapiensMutation(s): 0 
Gene Names: KIT (SCFR)
EC: 2.7.10.1
Find proteins for P10721 (Homo sapiens)
Go to Gene View: KIT
Go to UniProtKB:  P10721
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
0LI
Query on 0LI

Download SDF File 
Download CCD File 
A
3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzamide
Ponatinib
C29 H27 F3 N6 O
PHXJVRSECIGDHY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0LIIC50: <11 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.032α = 90.00
b = 70.032β = 90.00
c = 129.212γ = 120.00
Software Package:
Software NamePurpose
StructureStudiodata collection
HKL-2000data scaling
CNXrefinement
CNSrefinement
Quantamodel building
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-11-26
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Derived calculations, Other, Refinement description, Source and taxonomy