5K00 | pdb_00005k00

MELK in complex with NVS-MELK5

• PDB DOI: https://doi.org/10.2210/pdb5K00/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-05-17 Released: 2017-03-01 
• Deposition Author(s): Sprague, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.196 (Depositor), 0.193 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

"Addition" and "Subtraction": Selectivity Design for Type II Maternal Embryonic Leucine Zipper Kinase Inhibitors.

Chen, X., Giraldes, J., Sprague, E.R., Shakya, S., Chen, Z., Wang, Y., Joud, C., Mathieu, S., Chen, C.H., Straub, C., Duca, J., Hurov, K., Yuan, Y., Shao, W., Toure, B.B.

(2017) J Med Chem 60: 2155-2161

• PubMed: 28186750 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00033
• Primary Citation Related Structures: 
  5K00


• PubMed Abstract: 
  

  While adding the structural features that are more favored by on-target activity is the more common strategy in selectivity optimization, the opposite strategy of subtracting the structural features that contribute more to off-target activity can also be very effective. Reported here is our successful effort of improving the kinase selectivity of type II maternal embryonic leucine zipper kinase inhibitors by applying these two complementary approaches together, which clearly demonstrates the powerful synergy between them.

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Organizational Affiliation: 
• Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139, United States.

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: 39.53 kDa 
• Atom Count: 2,841 
• Modeled Residue Count: 311 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal embryonic leucine zipper kinase	A	335	Homo sapiens	Mutation(s): 0  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 GTEx:  ENSG00000165304

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6PV	B [auth A]	4-{2-[(3-methoxyphenyl)amino]-4-[(piperidin-4-yl)methoxy]pyrimidin-5-yl}-N-[2-oxo-2-(phenylamino)ethyl]benzamide C32 H34 N6 O4 AJPBKLULISUYTP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.196 (Depositor), 0.193 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.471	α = 90
b = 67.403	β = 90
c = 104.625	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Sprague, E.R.

Revision History  

• Version 1.0: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2017-03-08
  Changes: Database references
• Version 1.2: 2017-03-15
  Changes: Database references
• Version 1.3: 2017-03-22
  Changes: Database references
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references