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

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1021/jm4013888
  • Primary Citation of Related Structures:  
    4MH7, 4MHA

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase Mer
A, B
313Homo sapiensMutation(s): 0 
Gene Names: MERMERTK
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
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MH7

Download Ideal Coordinates CCD File 
H [auth A]N-butyl-2-(butylamino)-4-[(trans-4-hydroxycyclohexyl)amino]-N-methylpyrimidine-5-carboxamide
C20 H35 N5 O2
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
Binding Affinity Annotations 
IDSourceBinding Affinity
MH7 BindingDB:  4MH7 IC50: 5900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.874α = 90
b = 90.864β = 99.98
c = 69.587γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description