4RCH

Discovery of 2-Pyridyl Ureas as Glucokinase Activators

• PDB DOI: https://doi.org/10.2210/pdb4RCH/pdb

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


• 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: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 

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: https://doi.org/10.1021/jm501204z
• Primary Citation of Related Structures:  
  4RCH


• 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.

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: 53.59 kDa 
• Atom Count: 3,569 
• Modelled Residue Count: 448 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	474	Homo sapiens	Mutation(s): 0  Gene Names: GCK EC: 2.7.1.2
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3LZ	C [auth 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
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3LZ	BindingDB:  4RCH	EC50: min: 88, max: 231 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.116	α = 90
b = 80.116	β = 90
c = 321.807	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary