5K0K

Crystal structure of the catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor UNC2434


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.545 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Design and Synthesis of Novel Macrocyclic Mer Tyrosine Kinase Inhibitors.

Wang, X.Liu, J.Zhang, W.Stashko, M.A.Nichols, J.Miley, M.J.Norris-Drouin, J.Chen, Z.Machius, M.DeRyckere, D.Wood, E.Graham, D.K.Earp, H.S.Kireev, D.Frye, S.V.

(2016) ACS Med Chem Lett 7: 1044-1049

  • DOI: 10.1021/acsmedchemlett.6b00221

  • PubMed Abstract: 
  • Mer tyrosine kinase (MerTK) is aberrantly elevated in various tumor cells and has a normal anti-inflammatory role in the innate immune system. Inhibition of MerTK may provide dual effects against these MerTK-expressing tumors through reducing cancer ...

    Mer tyrosine kinase (MerTK) is aberrantly elevated in various tumor cells and has a normal anti-inflammatory role in the innate immune system. Inhibition of MerTK may provide dual effects against these MerTK-expressing tumors through reducing cancer cell survival and redirecting the innate immune response. Recently, we have designed novel and potent macrocyclic pyrrolopyrimidines as MerTK inhibitors using a structure-based approach. The most active macrocycles had an EC50 below 40 nM in a cell-based MerTK phosphor-protein ELISA assay. The X-ray structure of macrocyclic analogue 3 complexed with MerTK was also resolved and demonstrated macrocycles binding in the ATP binding pocket of the MerTK protein as anticipated. In addition, the lead compound 16 (UNC3133) had a 1.6 h half-life and 16% oral bioavailability in a mouse PK study.


    Organizational Affiliation

    Center for Integrative Chemical Biology and Drug Discovery, 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
6Q1
Query on 6Q1

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Download CCD File 
A, B
15-{4-[(4-methylpiperazin-1-yl)methyl]phenyl}-4,5,6,7,9,10,11,12-octahydro-2,16-(azenometheno)pyrrolo[2,1-d][1,3,5,9]tetraazacyclotetradecin-8(3H)-one
UNC2434
C26 H35 N7 O
RYOJEPUQWYYQQK-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.545 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.072α = 90.00
b = 91.315β = 100.42
c = 69.203γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release