4D2W

Structure of MELK in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Fragment-Based Discovery of Type I Inhibitors of Maternal Embryonic Leucine Zipper Kinase

Johnson, C.N.Berdini, V.Beke, L.Bonnet, P.Brehmer, D.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.Mcmenamin, R.Patel, S.Rees, D.C.Sharff, A.Sommen, F.Wu, T.Linders, J.T.M.

(2015) ACS Med Chem Lett 6: 25

  • DOI: 10.1021/ml5001245
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Fragment-based drug design was successfully applied to maternal embryonic leucine zipper kinase (MELK). A low affinity (160 μM) fragment hit was identified, which bound to the hinge region with an atypical binding mode, and this was optimized using s ...

    Fragment-based drug design was successfully applied to maternal embryonic leucine zipper kinase (MELK). A low affinity (160 μM) fragment hit was identified, which bound to the hinge region with an atypical binding mode, and this was optimized using structure-based design into a low-nanomolar and cell-penetrant inhibitor, with a good selectivity profile, suitable for use as a chemical probe for elucidation of MELK biology.


    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 KINASEA, B, C, D356Homo sapiensMutation(s): 7 
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NF5
Query on NF5

Download CCD File 
A, B, C, D
4-bromo-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide
C17 H17 Br N2 O
YMOUEQZHQYODQT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NF5IC50:  31000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.956α = 85.74
b = 74.947β = 70.07
c = 78.216γ = 89.94
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection