MELK in complex with NVS-MELK8F

Experimental Data Snapshot

  • Resolution: 1.96 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


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: https://doi.org/10.1021/acs.jmedchem.6b00052
  • Primary Citation of Related Structures:  
    5IH8, 5IH9, 5IHA, 5IHC

  • 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-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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maternal embryonic leucine zipper kinase335Homo sapiensMutation(s): 0 
Gene Names: MELKKIAA0175
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6BE

Download Ideal Coordinates CCD File 
B [auth A]1-methyl-4-(4-{4-[3-(2-methylpropoxy)pyridin-4-yl]-1H-pyrazol-1-yl}phenyl)piperazine
C23 H29 N5 O
Binding Affinity Annotations 
IDSourceBinding Affinity
6BE BindingDB:  5IHA IC50: min: 9, max: 410 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.96 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.152α = 90
b = 67.633β = 90
c = 104.651γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references, Derived calculations