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


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/ml5001273
  • Primary Citation of Related Structures:  
    4UMT, 4UMU

  • 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-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

    Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASE356Homo sapiensMutation(s): 5 
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14680 (Homo sapiens)
Explore Q14680 
Go to UniProtKB:  Q14680
PHAROS:  Q14680
GTEx:  ENSG00000165304 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14680
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
47W
Query on 47W

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

Download Ideal Coordinates CCD File 
B [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
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



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other