4UMT

Structure of MELK in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Design of Type II Inhibitors Applied to Maternal Embryonic Leucine Zipper Kinase.

Johnson, C.N.Adelinet, C.Berdini, V.Beke, L.Bonnet, P.Brehmer, D.Calo, F.Coyle, J.E.Day, P.J.Frederickson, M.Freyne, E.J.E.Gilissen, R.A.H.J.Hamlett, C.C.F.Howard, S.Meerpoel, L.Mevellec, L.Mcmenamin, R.Pasquier, E.Patel, S.Rees, D.C.Linders, J.T.M.

(2015) ACS Med Chem Lett 6: 31

  • DOI: 10.1021/ml5001273
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A novel Type II kinase inhibitor chemotype has been identified for maternal embryonic leucine zipper kinase (MELK) using structure-based ligand design. The strategy involved structural characterization of an induced DFG-out pocket by protein-ligand X ...

    A novel Type II kinase inhibitor chemotype has been identified for maternal embryonic leucine zipper kinase (MELK) using structure-based ligand design. The strategy involved structural characterization of an induced DFG-out pocket by protein-ligand X-ray crystallography and incorporation of a slender linkage capable of bypassing a large gate-keeper residue, thus enabling design of molecules accessing both hinge and induced pocket regions. Optimization of an initial hit led to the identification of a low-nanomolar, cell-penetrant Type II inhibitor suitable for use as a chemical probe for MELK.


    Organizational Affiliation

    Janssen Research and Development, A Division of Janssen Pharmaceutica N.V. , Turnhoutseweg 30, Beerse 2340, Belgium.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASEA356Homo sapiensMutation(s): 5 
Gene Names: MELKKIAA0175
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
Find proteins for Q14680 (Homo sapiens)
Explore Q14680 
Go to UniProtKB:  Q14680
NIH Common Fund Data Resources
PHAROS  Q14680
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
47W
Query on 47W

Download CCD File 
A
1-(4-{[3-(isoquinolin-7-yl)prop-2-yn-1-yl]oxy}-2-methoxybenzyl)piperazinediium
C24 H27 N3 O2
SSBLXEABMBMHKV-UHFFFAOYSA-P
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.274α = 90
b = 103.274β = 90
c = 64.887γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references