4D2W

Structure of MELK in complex with inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb4D2W/pdb

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


• Deposited: 2014-05-13 Released: 2014-10-08 
• 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: 1.92 Å
• R-Value Free: 0.247 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Fragment-Based Discovery of Type I Inhibitors of Maternal Embryonic Leucine Zipper Kinase

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.

(2015) ACS Med Chem Lett 6: 25

• PubMed: 25589925 
• DOI: https://doi.org/10.1021/ml5001245
• Primary Citation of Related Structures:  
  4D2P, 4D2T, 4D2V, 4D2W, 4UMP, 4UMQ, 4UMR


• PubMed Abstract: 
  

  Fragment-based drug design was successfully applied to maternal embryonic leucine zipper kinase (MELK). A low affinity (160 μM) fragment hit was identified, which bound to the hinge region with an atypical binding mode, and this was optimized using structure-based design into a low-nanomolar and cell-penetrant inhibitor, with a good selectivity profile, suitable for use as a chemical probe for elucidation of MELK biology.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 164.89 kDa 
• Atom Count: 11,529 
• Modelled Residue Count: 1,276 
• Deposited Residue Count: 1,424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MATERNAL EMBRYONIC LEUCINE ZIPPER KINASE	A, B, C, D	356	Homo sapiens	Mutation(s): 7  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
NF5	E [auth A], F [auth B], G [auth C], H [auth D]	4-bromo-N-(2,3,4,5-tetrahydro-1H-3-benzazepin-7-yl)benzamide C17 H17 Br N2 O YMOUEQZHQYODQT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NF5	BindingDB:  4D2W	IC50: 3.10e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.247 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.956	α = 85.74
b = 74.947	β = 70.07
c = 78.216	γ = 89.94

Software Package:

Software Name	Purpose
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
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: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2018-04-04
  Changes: Data collection