7AW2

MerTK kinase domain with type 1.5 inhibitor from a DNA-encoded library


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Generating Selective Leads for Mer Kinase Inhibitors-Example of a Comprehensive Lead-Generation Strategy.

Nissink, J.W.M.Bazzaz, S.Blackett, C.Clark, M.A.Collingwood, O.Disch, J.S.Gikunju, D.Goldberg, K.Guilinger, J.P.Hardaker, E.Hennessy, E.J.Jetson, R.Keefe, A.D.McCoull, W.McMurray, L.Olszewski, A.Overman, R.Pflug, A.Preston, M.Rawlins, P.B.Rivers, E.Schimpl, M.Smith, P.Truman, C.Underwood, E.Warwicker, J.Winter-Holt, J.Woodcock, S.Zhang, Y.

(2021) J Med Chem 64: 3165-3184

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01904
  • Primary Citation of Related Structures:  
    7AVX, 7AVY, 7AVZ, 7AW0, 7AW1, 7AW2, 7AW3, 7AW4

  • PubMed Abstract: 

    Mer is a member of the TAM (Tyro3, Axl, Mer) kinase family that has been associated with cancer progression, metastasis, and drug resistance. Their essential function in immune homeostasis has prompted an interest in their role as modulators of antitumor immune response in the tumor microenvironment. Here we illustrate the outcomes of an extensive lead-generation campaign for identification of Mer inhibitors, focusing on the results from concurrent, orthogonal high-throughput screening approaches. Data mining, HT (high-throughput), and DECL (DNA-encoded chemical library) screens offered means to evaluate large numbers of compounds. We discuss campaign strategy and screening outcomes, and exemplify series resulting from prioritization of hits that were identified. Concurrent execution of HT and DECL screening successfully yielded a large number of potent, selective, and novel starting points, covering a range of selectivity profiles across the TAM family members and modes of kinase binding, and offered excellent start points for lead development.


  • Organizational Affiliation

    Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Mer298Homo sapiensMutation(s): 4 
Gene Names: MERTKMER
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12866 (Homo sapiens)
Explore Q12866 
Go to UniProtKB:  Q12866
PHAROS:  Q12866
GTEx:  ENSG00000153208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12866
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S4W (Subject of Investigation/LOI)
Query on S4W

Download Ideal Coordinates CCD File 
B [auth A]5-(2'-chloro-[1,1'-biphenyl]-4-yl)-N-(imidazo[1,2-a]pyridin-6-ylmethyl)-N-methyl-1,3,4-oxadiazol-2-amine
C23 H18 Cl N5 O
WPRJOLMYEVNSEK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.28α = 90
b = 94.35β = 90
c = 71.37γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references
  • Version 1.2: 2021-04-07
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description