4D2T

Structure of MELK in complex with inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 

wwPDB Validation 3D Report Full Report


This is version 2.0 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:  

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASE
A, B, C, D
356Homo sapiensMutation(s): 7 
Gene Names: MELK (KIAA0175)
EC: 2.7.11.1
Find proteins for Q14680 (Homo sapiens)
Go to Gene View: MELK
Go to UniProtKB:  Q14680
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3I7
Query on 3I7

Download SDF File 
Download CCD File 
A, B, C, D
3-[2-(phenylcarbamoyl)-5-(1H-pyrazol-4-yl)phenoxy]propan-1-aminium
C19 H21 N4 O2
KLMWPYHIMXLJIE-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.340 
  • R-Value Work: 0.270 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 66.526α = 86.03
b = 75.410β = 69.05
c = 79.736γ = 90.03
Software Package:
Software NamePurpose
BUSTERrefinement
d*TREKdata scaling
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references
  • Version 1.2: 2015-03-18
    Type: Refinement description
  • Version 2.0: 2018-04-04
    Type: Atomic model, Data collection