4CKR

Crystal structure of the human DDR1 kinase domain in complex with DDR1-IN-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Potent and Selective Ddr1 Receptor Tyrosine Kinase Inhibitor.

Kim, H.Tan, L.Weisberg, E.L.Liu, F.Canning, P.Choi, H.G.Ezell, S.A.Wu, H.Zhao, Z.Wang, J.Mandinova, A.Griffin, J.D.Bullock, A.N.Liu, Q.Lee, S.W.Gray, N.S.

(2013) Acs Chem.Biol. 8: 2145

  • DOI: 10.1021/cb400430t

  • PubMed Abstract: 
  • The DDR1 receptor tyrosine kinase is activated by matrix collagens and has been implicated in numerous cellular functions such as proliferation, differentiation, adhesion, migration, and invasion. Here we report the discovery of a potent and selectiv ...

    The DDR1 receptor tyrosine kinase is activated by matrix collagens and has been implicated in numerous cellular functions such as proliferation, differentiation, adhesion, migration, and invasion. Here we report the discovery of a potent and selective DDR1 inhibitor, DDR1-IN-1, and present the 2.2 Å DDR1 co-crystal structure. DDR1-IN-1 binds to DDR1 in the 'DFG-out' conformation and inhibits DDR1 autophosphorylation in cells at submicromolar concentrations with good selectivity as assessed against a panel of 451 kinases measured using the KinomeScan technology. We identified a mutation in the hinge region of DDR1, G707A, that confers >20-fold resistance to the ability of DDR1-IN-1 to inhibit DDR1 autophosphorylation and can be used to establish what pharmacology is DDR1-dependent. A combinatorial screen of DDR1-IN-1 with a library of annotated kinase inhibitors revealed that inhibitors of PI3K and mTOR such as GSK2126458 potentiate the antiproliferative activity of DDR1-IN-1 in colorectal cancer cell lines. DDR1-IN-1 provides a useful pharmacological probe for DDR1-dependent signal transduction.


    Organizational Affiliation

    Cutaneous Biology Research Center, Massachusetts General Hospital and Harvard Medical School , Charlestown, Massachusetts 02129, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
A
315Homo sapiensMutation(s): 0 
Gene 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
DI1
Query on DI1

Download SDF File 
Download CCD File 
A
4-[(4-ethylpiperazin-1-yl)methyl]-n-{4-methyl-3-[(2-oxo-2,3-dihydro-1h-indol-5-yl)oxy]phenyl}-3-(trifluoromethyl)benzamide
C30 H31 F3 N4 O3
AOZPVMOOEJAZGK-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DI1EC50: 86 nM (100) BINDINGDB
DI1IC50: 86 - 105 nM (100) BINDINGDB
DI1IC50: 105 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 59.308α = 90.00
b = 59.308β = 90.00
c = 178.490γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Data collection