Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 52160.95 
• Atom Count: 3344 
• Residue Count: 458 
• Unique protein chains: 1

5V4W

Human glucokinase in complex with novel indazole activator.

• DOI: 10.2210/pdb5V4W/pdb

• Classification: transferase/transferase activator
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-03-10 Released: 2017-05-31 
• Deposition Author(s): Skene, R.J., Hosfield, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 

Literature

Discovery of potent and orally active 1,4-disubstituted indazoles as novel allosteric glucokinase activators.

Cheruvallath, Z.S., Gwaltney, S.L., Sabat, M., Tang, M., Wang, H., Jennings, A., Hosfield, D., Lee, B., Wu, Y., Halkowycz, P., Grimshaw, C.E.

(2017) Bioorg. Med. Chem. Lett. 27: 2678-2682

• PubMed: 28512030 
• DOI: 10.1016/j.bmcl.2017.04.041
• Primary Citation of Related Structures:  
  5V4X


• PubMed Abstract: 
  

Guided by co-crystal structural information obtained from a different series we were exploring, a scaffold morphing and SBDD approach led to the discovery of the 1,4-disubstituted indazole series as a novel class of GKAs that potently activate GK in enzyme and cell assays. anti-diabetic OGTT efficacy was demonstrated with 29 in a rodent models of type 2 diabetes.

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Organizational Affiliation: 

Takeda California, 10410 Science Center Drive, San Diego 92121, USA. Electronic address: [e-mail].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Glucokinase	A	458	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
8WM	A	(2S)-2-[4-(cyclopropylsulfonyl)-1H-indazol-1-yl]-N-(5-fluoro-1,3-thiazol-2-yl)-3-(oxan-4-yl)propanamide C21 H23 F N4 O4 S2 VFUKAAVEACENGY-KRWDZBQOSA-N
IOD	A	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
GLC	A	ALPHA-D-GLUCOSE C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 49.709	α = 90.00
b = 78.873	β = 90.00
c = 120.333	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
HKL-2000	data reduction
HKL-2000	data scaling
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-10 
• Released Date: 2017-05-31 
• Deposition Author(s): Skene, R.J., Hosfield, D.J.

Revision History 

• Version 1.0: 2017-05-31
  Type: Initial release
• Version 1.1: 2017-06-07
  Type: Database references
• Version 1.2: 2017-11-22
  Type: Refinement description