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: 41.26 kDa 
• Atom Count: 2,785 
• Modelled Residue Count: 316 
• Deposited Residue Count: 356 
• Unique protein chains: 1

 4UMU

Structure of MELK in complex with inhibitors

• PDB DOI: 10.2210/pdb4UMU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-05-21 Released: 2014-10-22 
• Deposition Author(s): Johnson, C.N., Berdini, V., Beke, L., Bonnet, P., Brehmer, D., Coyle, J.E., Day, P.J., Frederickson, M., Freyne, E.J.E., Gilissen, R.A.H.J., Hamlett, C.C.F., Howard, S., Meerpoel, L., McMenamin, R., Patel, S., Rees, D.C., Sharff, A., Sommen, F., Wu, T., Linders, J.T.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Structure-Based Design of Type II Inhibitors Applied to Maternal Embryonic Leucine Zipper Kinase.

Johnson, C.N., Adelinet, C., Berdini, V., Beke, L., Bonnet, P., Brehmer, D., Calo, F., Coyle, J.E., Day, P.J., Frederickson, M., Freyne, E.J.E., Gilissen, R.A.H.J., Hamlett, C.C.F., Howard, S., Meerpoel, L., Mevellec, L., Mcmenamin, R., Pasquier, E., Patel, S., Rees, D.C., Linders, J.T.M.

(2015) ACS Med Chem Lett 6: 31

• PubMed: 25589926 
• DOI: 10.1021/ml5001273
• Primary Citation of Related Structures:  
  4UMT, 4UMU


• PubMed Abstract: 
  

A novel Type II kinase inhibitor chemotype has been identified for maternal embryonic leucine zipper kinase (MELK) using structure-based ligand design. The strategy involved structural characterization of an induced DFG-out pocket by protein-ligand X-ray crystallography and incorporation of a slender linkage capable of bypassing a large gate-keeper residue, thus enabling design of molecules accessing both hinge and induced pocket regions. Optimization of an initial hit led to the identification of a low-nanomolar, cell-penetrant Type II inhibitor suitable for use as a chemical probe for MELK.

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Organizational Affiliation: 

Janssen Research and Development, A Division of Janssen Pharmaceutica N.V. , Turnhoutseweg 30, Beerse 2340, Belgium.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASE	A	356	Homo sapiens	Mutation(s): 5  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0V0	B [auth A]	(2-ethoxy-4-{[3-(isoquinolin-7-yl)prop-2-yn-1-yl]oxy}phenyl)methanaminium C21 H21 N2 O2 LQPNDHUHBKXZAG-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.359	α = 90
b = 103.359	β = 90
c = 65.255	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Johnson, C.N., Berdini, V., Beke, L., Bonnet, P., Brehmer, D., Coyle, J.E., Day, P.J., Frederickson, M., Freyne, E.J.E., Gilissen, R.A.H.J., Hamlett, C.C.F., Howard, S., Meerpoel, L., McMenamin, R., Patel, S., Rees, D.C., Sharff, A., Sommen, F., Wu, T., Linders, J.T.M.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references