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 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucokinase469Homo sapiensMutation(s): 0 
Gene Names: GCK
EC: 2.7.1.2 (PDB Primary Data), 2.7.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P35557 (Homo sapiens)
Explore P35557 
Go to UniProtKB:  P35557
PHAROS:  P35557
GTEx:  ENSG00000106633 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35557
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
S41 BindingDB:  3S41 EC50: min: 188, max: 1090 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.01α = 90
b = 82.2β = 90
c = 86.16γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary