3H3C

Crystal structure of PYK2 in complex with Sulfoximine-substituted trifluoromethylpyrimidine analog

• PDB DOI:  https://doi.org/10.2210/pdb3H3C/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2009-04-16 Released: 2009-05-26 
• Deposition Author(s): Han, S., Mistry, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Sulfoximine-substituted trifluoromethylpyrimidine analogs as inhibitors of proline-rich tyrosine kinase 2 (PYK2) show reduced hERG activity.

Walker, D.P., Zawistoski, M.P., McGlynn, M.A., Li, J.C., Kung, D.W., Bonnette, P.C., Baumann, A., Buckbinder, L., Houser, J.A., Boer, J., Mistry, A., Han, S., Xing, L., Guzman-Perez, A.

(2009) Bioorg Med Chem Lett 19: 3253-3258

• PubMed: 19428251 
• DOI: https://doi.org/10.1016/j.bmcl.2009.04.093
• Primary Citation of Related Structures:  
  3H3C


• PubMed Abstract: 
  

The synthesis, in vitro properties, and in vivo pharmacokinetics for a series of sulfoximine-substituted trifluoromethylpyrimidines as inhibitors of proline-rich tyrosine kinase, a target for the possible treatment of osteoporosis, are described. These compounds were prepared as surrogates of the corresponding sulfone compound 1. Sulfone 1 was an attractive PYK2 lead compound; however, subsequent studies determined this compound possessed high dofetilide binding, which is an early indicator of cardiovascular safety. Surprisingly, the corresponding sulfoximine analogs displayed significantly lower dofetilide binding, which, for N-methylsulfoximine (S)-14a, translated to lower activity in a patch clamp hERG K(+) ion channel screen. In addition, compound (S)-14a shows good oral exposure in a rat pharmacokinetic model.

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Organizational Affiliation: 

Pfizer Global Research and Development, Eastern Point Road, Groton, CT 06340, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 33.13 kDa 
• Atom Count: 2,219 
• Modelled Residue Count: 263 
• Deposited Residue Count: 277 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein tyrosine kinase 2 beta	A	277	Homo sapiens	Mutation(s): 0  Gene Names: PTK2B, FAK2, PYK2, RAFTK EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14289 (Homo sapiens) Explore Q14289  Go to UniProtKB:  Q14289
PHAROS:  Q14289

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P1E	G [auth A]	4-{[4-{[(1R,2R)-2-(dimethylamino)cyclopentyl]amino}-5-(trifluoromethyl)pyrimidin-2-yl]amino}-N-methylbenzenesulfonamide C19 H25 F3 N6 O2 S CAUFYHKGKDJMQG-HZPDHXFCSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
P1E	BindingDB:  3H3C	IC50: min: 88, max: 154 (nM) from 3 assay(s)
	PDBBind:  3H3C	IC50: 140 (nM) from 1 assay(s)
	Binding MOAD:  3H3C	IC50: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.281	α = 90
b = 92.83	β = 92.64
c = 42.843	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Han, S., Mistry, A.

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance