4BKY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASE347Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14680
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
82B
Query on 82B

Download Ideal Coordinates CCD File 
B [auth A]3'-{[(4-bromo-1-methyl-1H-pyrrol-2-yl)carbonyl]amino}-N-[(1S)-1-phenyl-2-(pyrrolidin-1-yl)ethyl]-1',4'-dihydro-5'H-spiro[cyclopropane-1,6'-pyrrolo[3,4-c]pyrazole]-5'-carboxamide
C26 H30 Br N7 O2
FWWFONGGISSNJV-HXUWFJFHSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
C [auth A]UNKNOWN ATOM OR ION
X
Binding Affinity Annotations 
IDSourceBinding Affinity
82B PDBBind:  4BKY IC50: 12 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.979α = 90
b = 64.266β = 90
c = 92.649γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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