6BRJ

DDR1 bound to VX-680


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/10.1016/j.chembiol.2018.11.005
  • Primary Citation of Related Structures:  
    6BRJ, 6BSD

  • 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 more than 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Epithelial discoidin domain-containing receptor 1351Homo sapiensMutation(s): 0 
Gene Names: DDR1CAKEDDR1NEPNTRK4PTK3ARTK6TRKE
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q08345 (Homo sapiens)
Explore Q08345 
Go to UniProtKB:  Q08345
PHAROS:  Q08345
GTEx:  ENSG00000204580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08345
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VX6
Query on VX6

Download Ideal Coordinates CCD File 
B [auth A]CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE
C23 H28 N8 O S
GCIKSSRWRFVXBI-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VX6 BindingDB:  6BRJ Kd: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.5α = 90
b = 75.4β = 90
c = 77.237γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
autoPROCdata scaling
Cootmodel building
HKL-2000data collection
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM119437
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM108904
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30 CA008748
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM121505
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA58530

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2022-03-23
    Changes: Author supporting evidence, Database references, Refinement description
  • Version 2.0: 2023-04-12
    Changes: Advisory, Atomic model, Database references, Derived calculations, Experimental preparation, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-10-25
    Changes: Data collection