5V4W

Human glucokinase in complex with novel indazole activator.

• PDB DOI: https://doi.org/10.2210/pdb5V4W/pdb

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


• 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 
• R-Value Observed: 0.201 

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: https://doi.org/10.1016/j.bmcl.2017.04.041
• Primary Citation of Related Structures:  
  5V4W, 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].

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: 52.16 kDa 
• Atom Count: 3,569 
• Modelled Residue Count: 419 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	458	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8WM	C [auth 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
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
IOD	D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
8WM	BindingDB:  5V4W	EC50: 40 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.261 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.709	α = 90
b = 78.873	β = 90
c = 120.333	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references, Structure summary