5TWL

Structure of Maternal Embryonic Leucine Zipper Kinase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

MELK is not necessary for the proliferation of basal-like breast cancer cells.

Huang, H.T., Seo, H.S., Zhang, T., Wang, Y., Jiang, B., Li, Q., Buckley, D.L., Nabet, B., Roberts, J.M., Paulk, J., Dastjerdi, S., Winter, G.E., McLauchlan, H., Moran, J., Bradner, J.E., Eck, M.J., Dhe-Paganon, S., Zhao, J.J., Gray, N.S.

(2017) Elife 6

  • DOI: 10.7554/eLife.26693
  • Primary Citation of Related Structures:  
    5TWL, 5TWU, 5TWY, 5TWZ, 5TX3

  • PubMed Abstract: 

    • Thorough preclinical target validation is essential for the success of drug discovery efforts. In this study, we combined chemical and genetic perturbants, including the development of a novel selective maternal embryonic leucine zipper kinase (MELK) inhibitor HTH-01-091, CRISPR/Cas9-mediated MELK knockout, a novel chemical-induced protein degradation strategy, RNA interference and CRISPR interference to validate MELK as a therapeutic target in basal-like breast cancers (BBC) ...

    Thorough preclinical target validation is essential for the success of drug discovery efforts. In this study, we combined chemical and genetic perturbants, including the development of a novel selective maternal embryonic leucine zipper kinase (MELK) inhibitor HTH-01-091, CRISPR/Cas9-mediated MELK knockout, a novel chemical-induced protein degradation strategy, RNA interference and CRISPR interference to validate MELK as a therapeutic target in basal-like breast cancers (BBC). In common culture conditions, we found that small molecule inhibition, genetic deletion, or acute depletion of MELK did not significantly affect cellular growth. This discrepancy to previous findings illuminated selectivity issues of the widely used MELK inhibitor OTSSP167, and potential off-target effects of MELK-targeting short hairpins. The different genetic and chemical tools developed here allow for the identification and validation of any causal roles MELK may play in cancer biology, which will be required to guide future MELK drug discovery efforts. Furthermore, our study provides a general framework for preclinical target validation.

    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maternal embryonic leucine zipper kinaseA341Homo sapiensMutation(s): 0 
Gene Names: MELK, KIAA0175
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14680 (Homo sapiens)
Explore Q14680 
Go to UniProtKB:  Q14680
PHAROS:  Q14680
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14680
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H91
Query on H91
Download Ideal Coordinates CCD File 
B [auth A]9-(3,5-dichloro-4-hydroxyphenyl)-1-{trans-4-[(dimethylamino)methyl]cyclohexyl}-3,4-dihydropyrimido[5,4-c]quinolin-2(1H)-one
C26 H28 Cl2 N4 O2
FUVRHGKKWNNBJX-RHDGDCLCSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
H91 Binding MOAD:  5TWL IC50: 10.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.52α = 90
b = 68.3β = 90
c = 104.95γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata processing
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-22
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references