5K5N | pdb_00005k5n

Crystal structure of GSK-3beta complexed with PF-04802367, a highly selective brain-penetrant kinase inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5K5N/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-05-23 Released: 2016-09-21 
• Deposition Author(s): Kurumbail, R.G., Chang, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Discovery of a Highly Selective Glycogen Synthase Kinase-3 Inhibitor (PF-04802367) That Modulates Tau Phosphorylation in the Brain: Translation for PET Neuroimaging.

Liang, S.H., Chen, J.M., Normandin, M.D., Chang, J.S., Chang, G.C., Taylor, C.K., Trapa, P., Plummer, M.S., Para, K.S., Conn, E.L., Lopresti-Morrow, L., Lanyon, L.F., Cook, J.M., Richter, K.E., Nolan, C.E., Schachter, J.B., Janat, F., Che, Y., Shanmugasundaram, V., Lefker, B.A., Enerson, B.E., Livni, E., Wang, L., Guehl, N.J., Patnaik, D., Wagner, F.F., Perlis, R., Holson, E.B., Haggarty, S.J., El Fakhri, G., Kurumbail, R.G., Vasdev, N.

(2016) Angew Chem Int Ed Engl 55: 9601-9605

• PubMed: 27355874 
• DOI: https://doi.org/10.1002/anie.201603797
• Primary Citation Related Structures: 
  5K5N


• PubMed Abstract: 
  

  Glycogen synthase kinase-3 (GSK-3) regulates multiple cellular processes in diabetes, oncology, and neurology. N-(3-(1H-1,2,4-triazol-1-yl)propyl)-5-(3-chloro-4-methoxyphenyl)oxazole-4-carboxamide (PF-04802367 or PF-367) has been identified as a highly potent inhibitor, which is among the most selective antagonists of GSK-3 to date. Its efficacy was demonstrated in modulation of tau phosphorylation in vitro and in vivo. Whereas the kinetics of PF-367 binding in brain tissues are too fast for an effective therapeutic agent, the pharmacokinetic profile of PF-367 is ideal for discovery of radiopharmaceuticals for GSK-3 in the central nervous system. A (11) C-isotopologue of PF-367 was synthesized and preliminary PET imaging studies in non-human primates confirmed that we have overcome the two major obstacles for imaging GSK-3, namely, reasonable brain permeability and displaceable binding.

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Organizational Affiliation: 
• Gordon Center for Medical Imaging & Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital & Department of Radiology, Harvard Medical School, Boston, MA, 02114, USA.
Pfizer Worldwide Research and Development, Groton Laboratories, Eastern Point Road, Groton, CT, 06340, USA.
Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, MA, 02139, USA.
Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, MA, 02114, USA.
Stanley Center for Psychiatric Research, Broad Institute, 415 Main Street, Cambridge, MA, o2142, USA.
Pfizer Worldwide Research and Development, Groton Laboratories, Eastern Point Road, Groton, CT, 06340, USA. [e-mail].
Gordon Center for Medical Imaging & Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital & Department of Radiology, Harvard Medical School, Boston, MA, 02114, 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)

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: 85.17 kDa 
• Atom Count: 5,484 
• Modeled Residue Count: 667 
• Deposited Residue Count: 740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta	A, B	370	Homo sapiens	Mutation(s): 1  Gene Names: GSK3B EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841  Go to UniProtKB:  P49841
PHAROS:  P49841 GTEx:  ENSG00000082701

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QH	C [auth A], E [auth B]	5-(3-chloranyl-4-methoxy-phenyl)-~{N}-[3-(1,2,4-triazol-1-yl)propyl]-1,3-oxazole-4-carboxamide C16 H16 Cl N5 O3 RQFYFNAGNBUGFC-UHFFFAOYSA-N
SO4	D [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.293	α = 90
b = 99.907	β = 102.9
c = 66.91	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-21 
Deposition Author(s): Kurumbail, R.G., Chang, J.S.

Revision History  

• Version 1.0: 2016-09-21
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary