4L3Q

Crystal structure of glucokinase-activator complex


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • 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-ac ...

    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.


    Organizational Affiliation

    Cardiovascular, Metabolic, and Endocrine Diseases Chemistry, Pfizer Worldwide Research and Development, 620 Memorial Dr, Cambridge, MA 02139, USA. kevin.filipski@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
A
457Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
926
Query on 926

Download SDF File 
Download CCD File 
A
6-{3-[(1-methyl-1H-imidazol-2-yl)sulfanyl]phenyl}pyridin-2(1H)-one
C15 H13 N3 O S
YYWBGPHQPMDZEM-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
926EC50: 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 = 79.512α = 90.00
b = 79.512β = 90.00
c = 321.131γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MAR345dtbdata collection
CNXrefinement
CNXphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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