4UMR

Structure of MELK in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 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
  • Primary Citation of Related Structures:  
    4D2T, 4D2V, 4D2W, 4D2P, 4UMP, 4UMQ, 4UMR

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASEA356Homo sapiensMutation(s): 6 
Gene Names: MELKKIAA0175
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QBB
Query on QBB

Download Ideal Coordinates CCD File 
B [auth A]4-fluoro-N-(1,2,3,4-tetrahydroisoquinolin-7-yl)benzamide
C16 H15 F N2 O
PGZJYUJKVGSJFI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QBBIC50:  160000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.169 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.664α = 90
b = 102.664β = 90
c = 65.663γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-08
    Type: Initial release
  • Version 1.1: 2015-01-28
    Changes: Database references