MELK in complex with NVS-MELK5

Experimental Data Snapshot

  • Resolution: 1.77 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


"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

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00033
  • Primary Citation of Related Structures:  

  • 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.

  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Inc. , Cambridge, Massachusetts 02139, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maternal embryonic leucine zipper kinase335Homo sapiensMutation(s): 0 
Gene Names: MELKKIAA0175
EC: (PDB Primary Data), (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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6PV

Download Ideal Coordinates CCD File 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
6PV Binding MOAD:  5K00 IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.77 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.471α = 90
b = 67.403β = 90
c = 104.625γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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