Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 51626.67 
• Atom Count: 3531 
• Residue Count: 457 
• Unique protein chains: 1

4L3Q

Crystal structure of glucokinase-activator complex

• DOI: 10.2210/pdb4L3Q/pdb

• Classification: Transferase/transferase activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2013-06-06 Released: 2013-07-24 
• Deposition Author(s): Gajiwala, K.S., Filipski, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.304 
• R-Value Work: 0.254 

Literature

Pyrimidone-based series of glucokinase activators with alternative donor-acceptor motif.

Filipski, K.J., Guzman-Perez, A., Bian, J., Perreault, C., Aspnes, G.E., Didiuk, M.T., Dow, R.L., Hank, R.F., Jones, C.S., Maguire, R.J., Tu, M., Zeng, D., Liu, S., Knafels, J.D., Litchfield, J., Atkinson, K., Derksen, D.R., Bourbonais, F., Gajiwala, K.S., Hickey, M., Johnson, T.O., Humphries, P.S., Pfefferkorn, J.A.

(2013) Bioorg.Med.Chem.Lett. 23: 4571-4578

• PubMed: 23831135 
• DOI: 10.1016/j.bmcl.2013.06.036


• PubMed Abstract: 
  

Glucokinase activators are a class of experimental agents under investigation as a therapy for Type 2 diabetes mellitus. An X-ray crystal structure of a modestly potent agent revealed the potential to substitute the common heterocyclic amide donor-acceptor motif for a pyridone moiety. We have successfully demonstrated that both pyridone and pyrimidone heterocycles can be used as a potent donor-acceptor substituent. Several sub-micromolar analogs that possess the desired partial activator profile were synthesized and characterized. Unfortunately, the most potent activators suffered from sub-optimal pharmacokinetic properties. Nonetheless, these donor-acceptor motifs may find utility in other glucokinase activator series or beyond.

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Organizational Affiliation: 

Cardiovascular, Metabolic, and Endocrine Diseases Chemistry, Pfizer Worldwide Research and Development, 620 Memorial Dr, Cambridge, MA 02139, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucokinase	A	457	Homo sapiens	Mutation(s): 0  Gene Names: GCK EC: 2.7.1.2
Find proteins for P35557 (Homo sapiens) Go to Gene View: GCK Go to UniProtKB:  P35557

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
926	A	6-{3-[(1-methyl-1H-imidazol-2-yl)sulfanyl]phenyl}pyridin-2(1H)-one C15 H13 N3 O S YYWBGPHQPMDZEM-UHFFFAOYSA-N
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
926	EC50: 2000 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.304 
• R-Value Work: 0.254 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 79.512	α = 90.00
b = 79.512	β = 90.00
c = 321.131	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
MAR345dtb	data collection
CNX	refinement
CNX	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-06 
• Released Date: 2013-07-24 
• Deposition Author(s): Gajiwala, K.S., Filipski, K.J.

Revision History 

• Version 1.0: 2013-07-24
  Type: Initial release
• Version 1.1: 2013-08-07
  Type: Database references