4M3Q

Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC1917


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.718 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Pseudo-Cyclization through Intramolecular Hydrogen Bond Enables Discovery of Pyridine Substituted Pyrimidines as New Mer Kinase Inhibitors.

Zhang, W.Zhang, D.Stashko, M.A.Deryckere, D.Hunter, D.Kireev, D.Miley, M.J.Cummings, C.Lee, M.Norris-Drouin, J.Stewart, W.M.Sather, S.Zhou, Y.Kirkpatrick, G.Machius, M.Janzen, W.P.Earp, H.S.Graham, D.K.Frye, S.V.Wang, X.

(2013) J.Med.Chem. 56: 9683-9692

  • DOI: 10.1021/jm401387j

  • PubMed Abstract: 
  • Abnormal activation or overexpression of Mer receptor tyrosine kinase has been implicated in survival signaling and chemoresistance in many human cancers. Consequently, Mer is a promising novel cancer therapeutic target. A structure-based drug design ...

    Abnormal activation or overexpression of Mer receptor tyrosine kinase has been implicated in survival signaling and chemoresistance in many human cancers. Consequently, Mer is a promising novel cancer therapeutic target. A structure-based drug design approach using a pseudo-ring replacement strategy was developed and validated to discover a new family of pyridinepyrimidine analogues as potent Mer inhibitors. Through SAR studies, 10 (UNC2250) was identified as the lead compound for further investigation based on high selectivity against other kinases and good pharmacokinetic properties. When applied to live cells, 10 inhibited steady-state phosphorylation of endogenous Mer with an IC50 of 9.8 nM and blocked ligand-stimulated activation of a chimeric EGFR-Mer protein. Treatment with 10 also resulted in decreased colony-forming potential in rhabdoid and NSCLC tumor cells, thereby demonstrating functional antitumor activity. The results provide a rationale for further investigation of this compound for therapeutic application in patients with cancer.


    Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery and ‡Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase Mer
A, B
313Homo sapiensMutation(s): 0 
Gene Names: MERTK (MER)
EC: 2.7.10.1
Find proteins for Q12866 (Homo sapiens)
Go to Gene View: MERTK
Go to UniProtKB:  Q12866
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
24K
Query on 24K

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Download CCD File 
A, B
trans-4-{[2-(butylamino)-5-(pyridin-2-yl)pyrimidin-4-yl]amino}cyclohexanol
C19 H27 N5 O
DMDQOCLVSGUEJT-SHTZXODSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24KIC50: 17 nM (98) BINDINGDB
24KIC50: 17 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.718 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.243 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.924α = 90.00
b = 91.120β = 99.81
c = 69.699γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-11-27
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description