Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 33.32 kDa 
• Atom Count: 2605 
• Modelled Residue Count: 290 
• Deposited Residue Count: 290 
• Unique protein chains: 1

4U8Z

Crystal structure of MST3 with a pyrrolopyrimidine inhibitor (PF-06447475)

• DOI: 10.2210/pdb4U8Z/pdb

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


• Deposited: 2014-08-05 Released: 2015-03-18 
• Deposition Author(s): Jasti, J., Song, X., Griffor, M., Kurumbail, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 

Literature

Discovery and preclinical profiling of 3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile (PF-06447475), a highly potent, selective, brain penetrant, and in vivo active LRRK2 kinase inhibitor.

Henderson, J.L., Kormos, B.L., Hayward, M.M., Coffman, K.J., Jasti, J., Kurumbail, R.G., Wager, T.T., Verhoest, P.R., Noell, G.S., Chen, Y., Needle, E., Berger, Z., Steyn, S.J., Houle, C., Hirst, W.D., Galatsis, P.

(2015) J Med Chem 58: 419-432

• PubMed: 25353650 
• DOI: 10.1021/jm5014055
• Primary Citation of Related Structures:  
  4U8Z, 4W8D, 4W8E


• PubMed Abstract: 
  

Leucine rich repeat kinase 2 (LRRK2) has been genetically linked to Parkinson's disease (PD) by genome-wide association studies (GWAS). The most common LRRK2 mutation, G2019S, which is relatively rare in the total population, gives rise to increased kinase activity. As such, LRRK2 kinase inhibitors are potentially useful in the treatment of PD. We herein disclose the discovery and optimization of a novel series of potent LRRK2 inhibitors, focusing on improving kinome selectivity using a surrogate crystallography approach. This resulted in the identification of 14 (PF-06447475), a highly potent, brain penetrant and selective LRRK2 inhibitor which has been further profiled in in vivo safety and pharmacodynamic studies.

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Organizational Affiliation: 

Worldwide Medicinal Chemistry, ‡Neuroscience Research Unit, and §Pharmacokinetics, Dynamics, and Metabolism, Pfizer Worldwide R&D , 610 Main Street, Cambridge, Massachusetts 02139, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase 24	A	290	Homo sapiens	Mutation(s): 0  Gene Names: STK24, MST3, STK3 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6E0 (Homo sapiens) Explore Q9Y6E0  Go to UniProtKB:  Q9Y6E0
PHAROS:  Q9Y6E0 GTEx:  ENSG00000102572

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3FE (Subject of Investigation/LOI)	C [auth A]	3-[4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]benzonitrile C17 H15 N5 O BHTWDJBVZQBRKP-UHFFFAOYSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
3FE	BindingDB:  4U8Z	IC50: 178 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.222 
• R-Value Work: 0.190 
• R-Value Observed: 0.192 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.11	α = 90
b = 59.02	β = 93.76
c = 61.81	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2014-08-05 
• Released Date: 2015-03-18 
Deposition Author(s): Jasti, J., Song, X., Griffor, M., Kurumbail, R.G.

Revision History  

• Version 1.0: 2015-03-18
  Type: Initial release