5IH9

MELK in complex with NVS-MELK8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maternal embryonic leucine zipper kinaseA335Homo sapiensMutation(s): 0 
Gene Names: MELKKIAA0175
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (UniProt)
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
6BF (Subject of Investigation/LOI)
Query on 6BF

Download Ideal Coordinates CCD File 
B [auth A]1-methyl-4-[4-(4-{3-[(piperidin-4-yl)methoxy]pyridin-4-yl}-1H-pyrazol-1-yl)phenyl]piperazine
C25 H32 N6 O
BLFBSGVUERKSST-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
6BF Binding MOAD:  5IH9 Kd: 2 (nM) from 1 assay(s)
BindingDB:  5IH9 IC50: min: 2, max: 140 (nM) from 3 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.043α = 90
b = 67.697β = 90
c = 104.355γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
SCALAdata scaling
BUSTER-TNTrefinement
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: 2017-11-22
    Changes: Database references, Derived calculations, Refinement description