3IMX

Crystal Structure of human glucokinase in complex with a synthetic activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Investigation of functionally liver selective glucokinase activators for the treatment of type 2 diabetes.

Bebernitz, G.R.Beaulieu, V.Dale, B.A.Deacon, R.Duttaroy, A.Gao, J.Grondine, M.S.Gupta, R.C.Kakmak, M.Kavana, M.Kirman, L.C.Liang, J.Maniara, W.M.Munshi, S.Nadkarni, S.S.Schuster, H.F.Stams, T.St Denny, I.Taslimi, P.M.Vash, B.Caplan, S.L.

(2009) J.Med.Chem. 52: 6142-6152

  • DOI: 10.1021/jm900839k

  • PubMed Abstract: 
  • Type 2 diabetes is a polygenic disease which afflicts nearly 200 million people worldwide and is expected to increase to near epidemic levels over the next 10-15 years. Glucokinase (GK) activators are currently under investigation by a number of phar ...

    Type 2 diabetes is a polygenic disease which afflicts nearly 200 million people worldwide and is expected to increase to near epidemic levels over the next 10-15 years. Glucokinase (GK) activators are currently under investigation by a number of pharmaceutical companies with only a few reaching early clinical evaluation. A GK activator has the promise of potentially affecting both the beta-cells of the pancreas, by improving glucose sensitive insulin secretion, as well as the liver, by reducing uncontrolled glucose output and restoring post-prandial glucose uptake and storage as glycogen. Herein, we report our efforts on a sulfonamide chemotype with the aim to generate liver selective GK activators which culminated in the discovery of 3-cyclopentyl-N-(5-methoxy-thiazolo[5,4-b]pyridin-2-yl)-2-[4-(4-methyl-piperazine-1-sulfonyl)-phenyl]-propionamide (17c). This compound activated the GK enzyme (alphaK(a) = 39 nM) in vitro at low nanomolar concentrations and significantly reduced glucose levels during an oral glucose tolerance test in normal mice.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139, USA. greg.bebernitz@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
A
455Homo 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-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
B84
Query on B84

Download SDF File 
Download CCD File 
A
(2R)-3-cyclopentyl-N-(5-methoxy[1,3]thiazolo[5,4-b]pyridin-2-yl)-2-{4-[(4-methylpiperazin-1-yl)sulfonyl]phenyl}propanamide
C26 H33 N5 O4 S2
GMGMDWSPSKXMJH-OAQYLSRUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.500α = 90.00
b = 90.300β = 90.00
c = 116.200γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
CNSrefinement
HKL-2000data collection
CNXrefinement
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-08-11 
  • Released Date: 2009-10-06 
  • Deposition Author(s): Stams, T., Vash, B.

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description