3S41 | pdb_00003s41

Glucokinase in complex with activator and glucose

• PDB DOI: https://doi.org/10.2210/pdb3S41/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.246 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

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

• DOI: https://doi.org/10.1039/C1MD00116G

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 53.57 kDa 
• Atom Count: 3,771 
• Modeled Residue Count: 448 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	469	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
S41	D [auth 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
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding 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 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.01	α = 90
b = 82.2	β = 90
c = 86.16	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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