Crystal structure of unphosphorylated Maternal Embryonic Leucine zipper Kinase (MELK) in complex with a benzodipyrazole inhibitor

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Structural Insight Into Maternal Embryonic Leucine Zipper Kinase (Melk) Conformation and Inhibition Towards Structure- Based Drug Design.

Canevari, G.Re Depaolini, S.Cucchi, U.Bertrand, J.A.Casale, E.Perrera, C.Forte, B.Carpinelli, P.Felder, E.R.

(2013) Biochemistry 52: 6380

  • DOI: https://doi.org/10.1021/bi4005864
  • Primary Citation of Related Structures:  
    4BKY, 4BKZ

  • PubMed Abstract: 

    Maternal embryonic leucine zipper kinase (MELK) is upregulated in several types of tumor, including breast, prostate, and brain tumors. Its expression is generally associated with cell survival, cell proliferation, and resistance to apoptosis. Therefore, the potential of MELK inhibitors as therapeutic agents is recently attracting considerable interest. Here we report the first structures of MELK in complex with AMP-PNP and with nanomolar inhibitors. Our studies shed light on the role of the MELK UBA domain, provide a characterization of the kinase active site, and identify key residues for achieving high potency, laying the groundwork for structure-based drug design efforts.

  • Organizational Affiliation

    Nerviano Medical Sciences , Viale Pasteur 10, 20014 Nerviano, Milan, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EC: (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14680 (Homo sapiens)
Explore Q14680 
Go to UniProtKB:  Q14680
GTEx:  ENSG00000165304 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14680
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1WS

Download Ideal Coordinates CCD File 
B [auth A]N-(3-aminopropyl)-8-[(3-fluorophenyl)amino]-2,4,5,7-tetrahydropyrazolo[3,4-e]indazole-3-carboxamide
C18 H20 F N7 O
Binding Affinity Annotations 
IDSourceBinding Affinity
1WS PDBBind:  4BKZ IC50: 27 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.44α = 90
b = 63.15β = 90
c = 95.31γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2019-04-24
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description