5BVN

Fragment-based discovery of potent and selective DDR1/2 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Fragment-Based Discovery of Potent and Selective DDR1/2 Inhibitors.

Murray, C.W.Berdini, V.Buck, I.M.Carr, M.E.Cleasby, A.Coyle, J.E.Curry, J.E.Day, J.E.Day, P.J.Hearn, K.Iqbal, A.Lee, L.Y.Martins, V.Mortenson, P.N.Munck, J.M.Page, L.W.Patel, S.Roomans, S.Smith, K.Tamanini, E.Saxty, G.

(2015) Acs Med.Chem.Lett. 6: 798-803

  • DOI: 10.1021/acsmedchemlett.5b00143
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either ...

    The DDR1 and DDR2 receptor tyrosine kinases are activated by extracellular collagen and have been implicated in a number of human diseases including cancer. We performed a fragment-based screen against DDR1 and identified fragments that bound either at the hinge or in the back pocket associated with the DFG-out conformation of the kinase. Modeling based on crystal structures of potent kinase inhibitors facilitated the "back-to-front" design of potent DDR1/2 inhibitors that incorporated one of the DFG-out fragments. Further optimization led to low nanomolar, orally bioavailable inhibitors that were selective for DDR1 and DDR2. The inhibitors were shown to potently inhibit DDR2 activity in cells but in contrast to unselective inhibitors such as dasatinib, they did not inhibit proliferation of mutant DDR2 lung SCC cell lines.


    Organizational Affiliation

    Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epithelial discoidin domain-containing receptor 1
A
324Homo 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
4VD
Query on 4VD

Download SDF File 
Download CCD File 
A
N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide
C23 H20 F N5 O2
ZPVUIOVIUFJGHO-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.328 
  • R-Value Work: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.040α = 90.00
b = 78.497β = 90.00
c = 74.499γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release