4MH7

Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC1896


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Mer specific tyrosine kinase inhibitors for the treatment and prevention of thrombosis.

Zhang, W.McIver, A.L.Stashko, M.A.DeRyckere, D.Branchford, B.R.Hunter, D.Kireev, D.Miley, M.J.Norris-Drouin, J.Stewart, W.M.Lee, M.Sather, S.Zhou, Y.Di Paola, J.A.Machius, M.Janzen, W.P.Earp, H.S.Graham, D.K.Frye, S.V.Wang, X.

(2013) J.Med.Chem. 56: 9693-9700

  • DOI: 10.1021/jm4013888
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The role of Mer kinase in regulating the second phase of platelet activation generates an opportunity to use Mer inhibitors for preventing thrombosis with diminished likelihood for bleeding as compared to current therapies. Toward this end, we have d ...

    The role of Mer kinase in regulating the second phase of platelet activation generates an opportunity to use Mer inhibitors for preventing thrombosis with diminished likelihood for bleeding as compared to current therapies. Toward this end, we have discovered a novel, Mer kinase specific substituted-pyrimidine scaffold using a structure-based drug design and a pseudo ring replacement strategy. The cocrystal structure of Mer with two compounds (7 and 22) possessing distinct activity have been determined. Subsequent SAR studies identified compound 23 (UNC2881) as a lead compound for in vivo evaluation. When applied to live cells, 23 inhibits steady-state Mer kinase phosphorylation with an IC50 value of 22 nM. Treatment with 23 is also sufficient to block EGF-mediated stimulation of a chimeric receptor containing the intracellular domain of Mer fused to the extracellular domain of EGFR. In addition, 23 potently inhibits collagen-induced platelet aggregation, suggesting that this class of inhibitors may have utility for prevention and/or treatment of pathologic thrombosis.


    Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery ‡Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy §Department of Pharmacology ∥Lineberger Comprehensive Cancer Center, Department of Medicine, School of Medicine, 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
MH7
Query on MH7

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Download CCD File 
A
N-butyl-2-(butylamino)-4-[(trans-4-hydroxycyclohexyl)amino]-N-methylpyrimidine-5-carboxamide
C20 H35 N5 O2
XUYGOTAWDBTFJQ-WKILWMFISA-N
 Ligand Interaction
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, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MH7IC50: 5900 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.874α = 90.00
b = 90.864β = 99.98
c = 69.587γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description