6JLR

Crystal structure of wild type MNK2 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.300 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Stepwise Evolution of Fragment Hits against MAPK Interacting Kinases 1 and 2.

Kwiatkowski, J.Liu, B.Pang, S.Ahmad, N.H.B.Wang, G.Poulsen, A.Yang, H.Poh, Y.R.Tee, D.H.Y.Ong, E.Retna, P.Dinie, N.Kwek, P.Wee, J.L.K.Manoharan, V.Low, C.B.Seah, P.G.Pendharkar, V.Sangthongpitag, K.Joy, J.Baburajendran, N.Jansson, A.E.Nacro, K.Hill, J.Keller, T.H.Hung, A.W.

(2020) J Med Chem 63: 621-637

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01582
  • Primary Citation of Related Structures:  
    6JLR

  • PubMed Abstract: 

    Dysregulation of translation initiation factor 4E (eIF4E) activity occurs in various cancers. Mitogen-activated protein kinase (MAPK) interacting kinases 1 and 2 (MNK1 and MNK2) play a fundamental role in activation of eIF4E. Structure-activity relationship-driven expansion of a fragment hit led to discovery of dual MNK1 and MNK2 inhibitors based on a novel pyridine-benzamide scaffold. The compounds possess promising in vitro and in vivo pharmacokinetic profiles and show potent on target inhibition of eIF4E phosphorylation in cells.


  • Organizational Affiliation

    Experimental Drug Development Centre, Agency for Science, Technology and Research (A*STAR) , 10 Biopolis Way, Chromos #05-01/06 , 138670 Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MAP kinase-interacting serine/threonine-protein kinase 2316Homo sapiensMutation(s): 0 
Gene Names: MKNK2GPRK7MNK2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HBH9 (Homo sapiens)
Explore Q9HBH9 
Go to UniProtKB:  Q9HBH9
PHAROS:  Q9HBH9
GTEx:  ENSG00000099875 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HBH9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BV9
Query on BV9

Download Ideal Coordinates CCD File 
B [auth A]4-[5-(1-methylpyrazol-4-yl)pyridin-3-yl]benzamide
C16 H14 N4 O
MUFGPGISRVJPDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.351 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.300 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.111α = 90
b = 105.111β = 90
c = 72.198γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata 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: 2020-02-12
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description