3S41

Glucokinase in complex with activator and glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Designing glucokinase activators with reduced hypoglycemia risk: discovery of N,N-dimethyl-5-(2-methyl-6-((5-methylpyrazin-2-yl)-carbamoyl)benzofuran-4-yloxy)pyrimidine-2-carboxamide as a clinical candidate for the treatment of type 2 diabetes mellitus

Pfefferkorn, J.A.Guzman-Perez, A.Oates, P.J.Litchfield, J.Aspnes, G.Basak, A.Benbow, J.Berliner, M.A.Bian, J.Choi, C.Freeman-Cook, K.Corbett, J.W.Didiuk, M.Dunetz, J.R.Filipski, K.J.Hungerford, W.M.Jones, C.S.Karki, K.Ling, A.Li, J.-C.Patel, L.Perreault, C.Risley, H.Saenz, J.Song, W.Tu, M.Aiello, R.Atkinson, K.Barucci, N.Beebe, D.Bourassa, P.Bourbounais, F.Brodeur, A.M.Burbey, R.Chen, J.D'Aquila, T.Derksen, D.R.Haddish-Berhane, N.Huang, C.Landro, J.Lapworth, A.L.MacDougall, M.Perregaux, D.Pettersen, J.Robertson, A.Tan, B.Treadway, J.L.Liu, S.Qiu, X.Knafels, J.Ammirati, M.Song, X.DaSilva-Jardine, P.Liras, S.Sweet, L.Rolph, T.P.

(2011) MEDCHEMCOMM 2: 828-839


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucokinase
A
469Homo 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
S41
Query on S41

Download SDF File 
Download CCD File 
A
N,N-dimethyl-5-({2-methyl-6-[(5-methylpyrazin-2-yl)carbamoyl]-1-benzofuran-4-yl}oxy)pyrimidine-2-carboxamide
C22 H20 N6 O4
MASKQITXHVYVFL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
S41EC50: 188 - 900 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.010α = 90.00
b = 82.200β = 90.00
c = 86.160γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-05-18 
  • Released Date: 2011-09-14 
  • Deposition Author(s): Liu, S.

Revision History 

  • Version 1.0: 2011-09-14
    Type: Initial release