5MAG | pdb_00005mag

Crystal structure of MELK in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5MAG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-11-03 Released: 2017-12-06 
• Deposition Author(s): Canevari, G., Re Depaolini, S., Casale, E., Felder, E., Kuster, B., Heinzlmeir, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: other

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

• PubMed: 29191878 
• DOI: https://doi.org/10.1126/science.aan4368
• Primary Citation Related Structures: 
  5LBW, 5LBY, 5LBZ, 5M5A, 5MAF, 5MAG, 5MAH, 5MAI


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.88 kDa 
• Atom Count: 2,698 
• Modeled Residue Count: 314 
• Deposited Residue Count: 347 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal embryonic leucine zipper kinase	A	347	Homo sapiens	Mutation(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 GTEx:  ENSG00000165304

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7KC	B [auth A]	PF-3758309 C25 H30 N8 O S AYCPARAPKDAOEN-LJQANCHMSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.252 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.18	α = 90
b = 62.81	β = 90
c = 94.11	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Canevari, G., Re Depaolini, S., Casale, E., Felder, E., Kuster, B., Heinzlmeir, S.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary