5IH9 | pdb_00005ih9

MELK in complex with NVS-MELK8A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.200 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5IH9

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.6b00052
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 39.39 kDa 
  • Atom Count: 2,874 
  • Modeled Residue Count: 308 
  • Deposited Residue Count: 335 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maternal embryonic leucine zipper kinase335Homo 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
GTEx:  ENSG00000165304 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14680
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6BF

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
Binding Affinity Annotations 
IDSourceBinding Affinity
6BF 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 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
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
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references