4BKY

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

• PDB DOI: https://doi.org/10.2210/pdb4BKY/pdb

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


• Deposited: 2013-04-30 Released: 2013-08-21 
• Deposition Author(s): Canevari, G., Re Depaolini, S., Cucchi, U., Forte, B., Carpinelli, P., Bertrand, J.A.

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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

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

• PubMed: 23914841 
• 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.

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Organizational Affiliation: 

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

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: 40.77 kDa 
• Atom Count: 2,771 
• Modelled Residue Count: 311 
• 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  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
82B	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	C [auth A]	UNKNOWN ATOM OR ION X

Binding Affinity Annotations
ID	Source	Binding 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 = 59.979	α = 90
b = 64.266	β = 90
c = 92.649	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-21 
Deposition Author(s): Canevari, G., Re Depaolini, S., Cucchi, U., Forte, B., Carpinelli, P., Bertrand, J.A.

Revision History  

• 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