6BSD

DDR1 bound to Dasatinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.606 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

What Makes a Kinase Promiscuous for Inhibitors?

Hanson, S.M.Georghiou, G.Thakur, M.K.Miller, W.T.Rest, J.S.Chodera, J.D.Seeliger, M.A.

(2019) Cell Chem Biol 26: 390-399.e5

  • DOI: 10.1016/j.chembiol.2018.11.005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ATP-competitive kinase inhibitors often bind several kinases due to the high conservation of the ATP binding pocket. Through clustering analysis of a large kinome profiling dataset, we found a cluster of eight promiscuous kinases that on average bind ...

    ATP-competitive kinase inhibitors often bind several kinases due to the high conservation of the ATP binding pocket. Through clustering analysis of a large kinome profiling dataset, we found a cluster of eight promiscuous kinases that on average bind more thanĀ five times more kinase inhibitors than the other 398 kinases in the dataset. To understand the structural basis of promiscuous inhibitor binding, we determined the co-crystal structure of the receptor tyrosine kinase DDR1 with the type I inhibitors dasatinib and VX-680. Surprisingly, we find that DDR1 binds these type I inhibitors in an inactive conformation typically reserved for type II inhibitors. Our computational and biochemical studies show that DDR1 is unusually stable in this inactive conformation, giving a mechanistic explanation for inhibitor promiscuity. This phenotypic clustering analysis provides a strategy to obtain functional insights not available by sequence comparison alone.


    Organizational Affiliation

    Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, USA.,Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY 11794-8651, USA.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA. Electronic address: markus.seeliger@stonybrook.edu.,Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA. Electronic address: john.chodera@choderalab.org.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA; Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065-1115, USA.,Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epithelial discoidin domain-containing receptor 1
A
876Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N1
Query on 1N1

Download SDF File 
Download CCD File 
A
N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
Dasatinib
C22 H26 Cl N7 O2 S
ZBNZXTGUTAYRHI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.606 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.669α = 90.00
b = 72.342β = 90.00
c = 74.656γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
AutoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2019-06-19
    Type: Data collection, Database references