Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 53587.82 
• Atom Count: 3544 
• Residue Count: 474 
• Unique protein chains: 1

4RCH

Discovery of 2-Pyridyl Ureas as Glucokinase Activators

• DOI: 10.2210/pdb4RCH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2014-09-16 Released: 2014-10-08 
• Deposition Author(s): Voegtli, W., Vigers, G.P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 

Literature

Discovery of 2-pyridylureas as glucokinase activators.

Hinklin, R.J., Aicher, T.D., Anderson, D.A., Baer, B.R., Boyd, S.A., Condroski, K.R., DeWolf, W.E., Kraser, C.F., McVean, M., Rhodes, S.P., Sturgis, H.L., Voegtli, W.C., Williams, L., Houze, J.B.

(2014) J.Med.Chem. 57: 8180-8186

• PubMed: 25203462 
• DOI: 10.1021/jm501204z


• PubMed Abstract: 
  

Glucokinase (GK) is the rate-limiting step for insulin release from the pancreas in response to high levels of glucose. Flux through GK also contributes to reducing hepatic glucose output. Since many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, identifying compounds that can allosterically activate GK may address this issue. Herein we report the identification and initial optimization of a novel series of glucokinase activators (GKAs). Optimization led to the identification of 33 as a compound that displayed activity in an oral glucose tolerance test (OGTT) in normal and diabetic mice.

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Organizational Affiliation: 

Array BioPharma Inc. , 3200 Walnut Street, Boulder, Colorado 80301, United States.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucokinase	A	474	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
3LZ	A	1-{3-[(2-ethylpyridin-3-yl)oxy]-5-(pyridin-2-ylsulfanyl)pyridin-2-yl}-3-methylurea C19 H19 N5 O2 S PIGWQTQWPKNWHF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3LZ	EC50: 88 - 231 nM (100) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 80.116	α = 90.00
b = 80.116	β = 90.00
c = 321.807	γ = 120.00

Software Package:

Software Name	Purpose
CrystalClear	data reduction
REFMAC	refinement
MOLREP	phasing
ADSC	data collection
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-09-16 
• Released Date: 2014-10-08 
• Deposition Author(s): Voegtli, W., Vigers, G.P.A.

Revision History 

• Version 1.0: 2014-10-08
  Type: Initial release
• Version 1.1: 2014-10-22
  Type: Database references