4BKJ

Crystal structure of the human DDR1 kinase domain in complex with imatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Mechanisms Determining Inhibition of the Collagen Receptor Ddr1 by Selective and Multi-Targeted Type II Kinase Inhibitors

Canning, P.Elkins, J.M.Goubin, S.Mahajan, P.Krojer, T.Vollmar, M.von Delft, F.Arrowsmith, C.H.Edwards, A.M.Bountra, C.Bullock, A.

(2014) J.Mol.Biol. 426: 2457

  • DOI: 10.1016/j.jmb.2014.04.014
  • Primary Citation of Related Structures:  3ZOS

  • PubMed Abstract: 
  • The discoidin domain receptors (DDRs), DDR1 and DDR2, form a unique subfamily of receptor tyrosine kinases that are activated by the binding of triple-helical collagen. Excessive signaling by DDR1 and DDR2 has been linked to the progression of variou ...

    The discoidin domain receptors (DDRs), DDR1 and DDR2, form a unique subfamily of receptor tyrosine kinases that are activated by the binding of triple-helical collagen. Excessive signaling by DDR1 and DDR2 has been linked to the progression of various human diseases, including fibrosis, atherosclerosis and cancer. We report the inhibition of these unusual receptor tyrosine kinases by the multi-targeted cancer drugs imatinib and ponatinib, as well as the selective type II inhibitor DDR1-IN-1. Ponatinib is identified as the more potent molecule, which inhibits DDR1 and DDR2 with an IC50 of 9nM. Co-crystal structures of human DDR1 reveal a DFG-out conformation (DFG, Asp-Phe-Gly) of the kinase domain that is stabilized by an unusual salt bridge between the activation loop and αD helix. Differences to Abelson kinase (ABL) are observed in the DDR1 P-loop, where a β-hairpin replaces the cage-like structure of ABL. P-loop residues in DDR1 that confer drug resistance in ABL are therefore accommodated outside the ATP pocket. Whereas imatinib and ponatinib bind potently to both the DDR and ABL kinases, the hydrophobic interactions of the ABL P-loop appear poorly satisfied by DDR1-IN-1 suggesting a structural basis for its DDR1 selectivity. Such inhibitors may have applications in clinical indications of DDR1 and DDR2 overexpression or mutation, including lung cancer.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
A, B
315Homo sapiensGene Names: DDR1 (CAK, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE)
EC: 2.7.10.1
Find proteins for Q08345 (Homo sapiens)
Go to Gene View: DDR1
Go to UniProtKB:  Q08345
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
STI
Query on STI

Download SDF File 
Download CCD File 
A, B
4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
STI-571;IMATINIB
C29 H31 N7 O
KTUFNOKKBVMGRW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STIIC50: 43 - 31000 nM (100) BINDINGDB
STIKd: 0.7 - 700 nM (100) BINDINGDB
STIIC50: 41 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.074α = 90.00
b = 60.074β = 90.00
c = 180.575γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2014-04-23
    Type: Database references
  • Version 1.2: 2014-05-07
    Type: Database references
  • Version 1.3: 2014-06-18
    Type: Database references
  • Version 1.4: 2018-01-24
    Type: Database references