5KZ8 | pdb_00005kz8

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

• PDB DOI: https://doi.org/10.2210/pdb5KZ8/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free: 
  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

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

• PubMed: 27816515 
• DOI: https://doi.org/10.1016/j.bmcl.2016.08.068
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA. Electronic address: [e-mail].
Department of Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
Department of Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
Department of In Vitro Sciences, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
Department of Drug Metabolism, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
Department of Neuroscience, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA.
Department of Structural Chemistry, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 80.88 kDa 
• Atom Count: 4,888 
• Modeled Residue Count: 602 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase MARK2	A, B	346	Homo sapiens	Mutation(s): 0  Gene Names: MARK2, EMK1 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 GTEx:  ENSG00000072518

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6Z5	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.21 Å
• R-Value Free:  0.290 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.416	α = 90
b = 120.416	β = 90
c = 99.457	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references