5KZ8

Mark2 complex with 7-[(1S)-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(3-pyridylamino)pyrrolo[2,3-d]pyrimidin-6-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure guided design of a series of selective pyrrolopyrimidinone MARK inhibitors.

Katz, J.D.Haidle, A.Childers, K.K.Zabierek, A.A.Jewell, J.P.Hou, Y.Altman, M.D.Szewczak, A.Chen, D.Harsch, A.Hayashi, M.Warren, L.Hutton, M.Nuthall, H.Su, H.P.Munshi, S.Stanton, M.G.Davies, I.W.Munoz, B.Northrup, A.

(2017) Bioorg Med Chem Lett 27: 114-120

  • DOI: 10.1016/j.bmcl.2016.08.068
  • Primary Citation of Related Structures:  
    5KZ7, 5KZ8

  • PubMed Abstract: 
  • The initial structure activity relationships around an isoindoline uHTS hit will be described. Information gleaned from ligand co-crystal structures allowed for rapid refinements in both MARK potency and kinase selectivity. These efforts allowed for the identification of a compound with properties suitable for use as an in vitro tool compound for validation studies on MARK as a viable target for Alzheimer's disease ...

    The initial structure activity relationships around an isoindoline uHTS hit will be described. Information gleaned from ligand co-crystal structures allowed for rapid refinements in both MARK potency and kinase selectivity. These efforts allowed for the identification of a compound with properties suitable for use as an in vitro tool compound for validation studies on MARK as a viable target for Alzheimer's disease.


    Organizational Affiliation

    Department of Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase MARK2A, B346Homo sapiensMutation(s): 0 
Gene Names: MARK2EMK1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.26 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZI7 (Homo sapiens)
Explore Q7KZI7 
Go to UniProtKB:  Q7KZI7
PHAROS:  Q7KZI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7KZI7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6Z5
Query on 6Z5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
5,5-dimethyl-7-[(1~{S})-4-oxidanyl-1~{H}-inden-1-yl]-2-phenylazanyl-pyrrolo[2,3-d]pyrimidin-6-one
C23 H20 N4 O2
XYYZSCWSVMFLOM-SFHVURJKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.416α = 90
b = 120.416β = 90
c = 99.457γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2016-07-23 
  • Released Date: 2017-05-31 
  • Deposition Author(s): Su, H.P., Munshi, S.K.

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-31
    Type: Initial release