5MAH

Crystal structure of MELK in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    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 ...

    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

    Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), TUM, Freising, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maternal embryonic leucine zipper kinaseA347Homo sapiensMutation(s): 0 
Gene Names: MELKKIAA0175
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7KD
Query on 7KD

Download Ideal Coordinates CCD File 
B [auth A]~{N}-methyl-4-[[4-[[3-[methyl(methylsulfonyl)amino]pyrazin-2-yl]methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide
C20 H21 F3 N8 O3 S
FWLMVFUGMHIOAA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.667α = 90
b = 63.704β = 90
c = 90.945γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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