5IH8

MELK in complex with NVS-MELK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Toward the Validation of Maternal Embryonic Leucine Zipper Kinase: Discovery, Optimization of Highly Potent and Selective Inhibitors, and Preliminary Biology Insight.

Toure, B.B.Giraldes, J.Smith, T.Sprague, E.R.Wang, Y.Mathieu, S.Chen, Z.Mishina, Y.Feng, Y.Yan-Neale, Y.Shakya, S.Chen, D.Meyer, M.Puleo, D.Brazell, J.T.Straub, C.Sage, D.Wright, K.Yuan, Y.Chen, X.Duca, J.Kim, S.Tian, L.Martin, E.Hurov, K.Shao, W.

(2016) J.Med.Chem. 59: 4711-4723

  • DOI: 10.1021/acs.jmedchem.6b00052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MELK kinase has been implicated in playing an important role in tumorigenesis. Our previous studies suggested that MELK is involved in the regulation of cell cycle and its genetic depletion leads to growth inhibition in a subset of high MELK-expressi ...

    MELK kinase has been implicated in playing an important role in tumorigenesis. Our previous studies suggested that MELK is involved in the regulation of cell cycle and its genetic depletion leads to growth inhibition in a subset of high MELK-expressing basal-like breast cancer cell lines. Herein we describe the discovery and optimization of novel MELK inhibitors 8a and 8b that recapitulate the cellular effects observed by short hairpin ribonucleic acid (shRNA)-mediated MELK knockdown in cellular models. We also discovered a novel fluorine-induced hydrophobic collapse that locked the ligand in its bioactive conformation and led to a 20-fold gain in potency. These novel pharmacological inhibitors achieved high exposure in vivo and were well tolerated, which may allow further in vivo evaluation.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maternal embryonic leucine zipper kinase
A
335Homo sapiensMutation(s): 0 
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
6BJ
Query on 6BJ

Download SDF File 
Download CCD File 
A
N-[(pyridin-2-yl)methyl]-4-[4-(pyridin-4-yl)-1H-pyrazol-1-yl]benzamide
C21 H17 N5 O
UKGSBPKSNSXMDN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6BJIC50: 180 - 18800 nM (99) BINDINGDB
6BJIC50: 180 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.550α = 90.00
b = 67.360β = 90.00
c = 105.340γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XDSdata scaling
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description