5MAI

Crystal structure of MELK in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The target landscape of clinical kinase drugs.

Klaeger, S.Heinzlmeir, S.Wilhelm, M.Polzer, H.Vick, B.Koenig, P.A.Reinecke, M.Ruprecht, B.Petzoldt, S.Meng, C.Zecha, J.Reiter, K.Qiao, H.Helm, D.Koch, H.Schoof, M.Canevari, G.Casale, E.Depaolini, S.R.Feuchtinger, A.Wu, Z.Schmidt, T.Rueckert, L.Becker, W.Huenges, J.Garz, A.K.Gohlke, B.O.Zolg, D.P.Kayser, G.Vooder, T.Preissner, R.Hahne, H.Tonisson, N.Kramer, K.Gotze, K.Bassermann, F.Schlegl, J.Ehrlich, H.C.Aiche, S.Walch, A.Greif, P.A.Schneider, S.Felder, E.R.Ruland, J.Medard, G.Jeremias, I.Spiekermann, K.Kuster, B.

(2017) Science 358: --

  • DOI: 10.1126/science.aan4368
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically e ...

    Kinase inhibitors are important cancer therapeutics. Polypharmacology is commonly observed, requiring thorough target deconvolution to understand drug mechanism of action. Using chemical proteomics, we analyzed the target spectrum of 243 clinically evaluated kinase drugs. The data revealed previously unknown targets for established drugs, offered a perspective on the "druggable" kinome, highlighted (non)kinase off-targets, and suggested potential therapeutic applications. Integration of phosphoproteomic data refined drug-affected pathways, identified response markers, and strengthened rationale for combination treatments. We exemplify translational value by discovering SIK2 (salt-inducible kinase 2) inhibitors that modulate cytokine production in primary cells, by identifying drugs against the lung cancer survival marker MELK (maternal embryonic leucine zipper kinase), and by repurposing cabozantinib to treat FLT3-ITD-positive acute myeloid leukemia. This resource, available via the ProteomicsDB database, should facilitate basic, clinical, and drug discovery research and aid clinical decision-making.


    Organizational Affiliation

    Department of Medicine III, Klinikum rechts der Isar, TUM, Munich, Germany.,Department of Pediatrics, Dr von Hauner Children's Hospital, LMU, Munich, Germany.,Department of Internal Medicine III, University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany.,Estonian Genome Center, University of Tartu, Tartu, Estonia.,Research Unit Analytical Pathology, Helmholtz Zentrum München, Neuherberg, Germany.,SAP SE, Potsdam, Germany.,Institut für Klinische Chemie und Pathobiochemie, TUM, Munich, Germany.,Structural Bioinformatics Group, Charité-Universitätsmedizin, Berlin, Germany.,Department of Chemistry, TUM, Garching, Germany.,Tartu University Hospital, Tartu, Estonia.,Oncology, Nerviano Medical Sciences Srl, Milan, Italy.,Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.,Center of Thoracic Surgery, Krefeld, Germany.,Center For Integrated Protein Science Munich (CIPSM), Munich, Germany.,Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany. kuster@tum.de.,Institute of Surgical Pathology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Apoptosis in Hematopoietic Stem Cells, Helmholtz Center Munich, German Center for Environmental Health (HMGU), Munich, Germany.,SAP SE, Walldorf, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maternal embryonic leucine zipper kinase
A
347Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
5U5
Query on 5U5

Download SDF File 
Download CCD File 
A
3-[(3~{Z})-3-[[[4-[(dimethylamino)methyl]phenyl]amino]-phenyl-methylidene]-2-oxidanylidene-1~{H}-indol-6-yl]-~{N}-ethyl-prop-2-ynamide
C29 H28 N4 O2
FLBNLJLONKAPLR-DQSJHHFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • Space Group: I 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 169.134α = 90.00
b = 169.134β = 90.00
c = 169.134γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references