4MLE | pdb_00004mle

Human Glucokinase in Complex with Novel Amino Thiazole Activator

• PDB DOI: https://doi.org/10.2210/pdb4MLE/pdb

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


• Deposited: 2013-09-06 Released: 2013-09-25 
• Deposition Author(s): Voegtli, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.289 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.231 (DCC) 

Literature

Identification of a New Class of Glucokinase Activators through Structure-Based Design.

Hinklin, R.J., Boyd, S.A., Chicarelli, M.J., Condroski, K.R., Dewolf, W.E., Lee, P.A., Lee, W., Singh, A., Thomas, L., Voegtli, W.C., Williams, L., Aicher, T.D.

(2013) J Med Chem 56: 7669-7678

• PubMed: 24015910 
• DOI: https://doi.org/10.1021/jm401116k
• Primary Citation Related Structures: 
  4MLE, 4MLH


• PubMed Abstract: 
  

  Glucose flux through glucokinase (GK) controls insulin release from the pancreas in response to high glucose concentrations. Glucose flux through GK also contributes to reducing hepatic glucose output. Because many individuals with type 2 diabetes appear to have an inadequacy or defect in one or both of these processes, compounds that can activate GK may serve as effective treatments for type 2 diabetes. Herein we report the identification and initial optimization of a novel series of allosteric glucokinase activators (GKAs). We discovered an initial thiazolylamino pyridine-based hit that was optimized using a structure-based design strategy and identified 26 as an early lead. Compound 26 demonstrated a good balance of in vitro potency and enzyme kinetic parameters and demonstrated blood glucose reductions in oral glucose tolerance tests in both C57BL/6J mice and high-fat fed Zucker diabetic fatty rats.

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Organizational Affiliation: 
• Array BioPharma , 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: 51.49 kDa 
• Atom Count: 3,538 
• Modeled Residue Count: 448 
• Deposited Residue Count: 455 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	455	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VO1	C [auth A]	3-(benzyloxy)-N-(4-methyl-1,3-thiazol-2-yl)pyridin-2-amine C16 H15 N3 O S LPJWCRSWBACCSH-UHFFFAOYSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VO1	BindingDB:  4MLE	EC50: min: 4940, max: 5800 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.289 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.231 (DCC) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.32	α = 90
b = 79.32	β = 90
c = 320.21	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Voegtli, W.C.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-10-23
  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: 2024-02-28
  Changes: Data collection, Database references, Structure summary