6E0E | pdb_00006e0e

Crystal structure of Glucokinase in complex with compound 6

• PDB DOI: https://doi.org/10.2210/pdb6E0E/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-06 Released: 2019-07-10 
• Deposition Author(s): Hinklin, R.J., Baer, B.R., Boyd, S.A., Chicarelli, M.D., Condroski, K.R., DeWolf, W.E., Fischer, J., Frank, M., Hingorani, G.P., Lee, P.A., Neitzel, N.A., Pratt, S.A., Singh, A., Sullivan, F.X., Turner, T., Voegtli, W.C., Wallace, E.M., Williams, L., Aicher, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Discovery and preclinical development of AR453588 as an anti-diabetic glucokinase activator.

Hinklin, R.J., Baer, B.R., Boyd, S.A., Chicarelli, M.D., Condroski, K.R., DeWolf Jr., W.E., Fischer, J., Frank, M., Hingorani, G.P., Lee, P.A., Neitzel, N.A., Pratt, S.A., Singh, A., Sullivan, F.X., Turner, T., Voegtli, W.C., Wallace, E.M., Williams, L., Aicher, T.D.

(2020) Bioorg Med Chem 28: 115232-115232

• PubMed: 31818630 
• DOI: https://doi.org/10.1016/j.bmc.2019.115232
• Primary Citation Related Structures: 
  6E0E, 6E0I


• PubMed Abstract: 
  

  Glucose flux through glucokinase (GK) controls insulin release from the pancreas in response to high levels of glucose. Flux through GK is also responsible for 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 activate GK could provide a therapeutic benefit. Herein we report the further structure activity studies of a novel series of glucokinase activators (GKA). These studies led to the identification of pyridine 72 as a potent GKA that lowered post-prandial glucose in normal C57BL/6J mice, and after 14d dosing in ob/ob mice.

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Organizational Affiliation: 
• Array BioPharma Inc., 3200 Walnut St., Boulder, CO 80301, United States. Electronic address: [e-mail].
Array BioPharma Inc., 3200 Walnut St., Boulder, CO 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: 50.75 kDa 
• Atom Count: 3,604 
• Modeled Residue Count: 448 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	448	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
HKM (Subject of Investigation/LOI)	C [auth A]	2-({2-[(4-methyl-1,3-thiazol-2-yl)amino]pyridin-3-yl}oxy)benzonitrile C16 H12 N4 O S KPJJEXKLZAXHEE-UHFFFAOYSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HKM	BindingDB:  6E0E	EC50: 2359 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.57	α = 90
b = 79.57	β = 90
c = 320.16	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Hinklin, R.J., Baer, B.R., Boyd, S.A., Chicarelli, M.D., Condroski, K.R., DeWolf, W.E., Fischer, J., Frank, M., Hingorani, G.P., Lee, P.A., Neitzel, N.A., Pratt, S.A., Singh, A., Sullivan, F.X., Turner, T., Voegtli, W.C., Wallace, E.M., Williams, L., Aicher, T.D.

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Structure summary