4ISG | pdb_00004isg

Human glucokinase in complex with novel activator (2S)-3-cyclohexyl-2-[4-(methylsulfonyl)-2-oxopiperazin-1-yl]-N-(1,3-thiazol-2-yl)propanamide

• PDB DOI: https://doi.org/10.2210/pdb4ISG/pdb

• Classification: TRANSFERASE/TRANSFERASE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2013-01-16 Released: 2013-03-20 
• Deposition Author(s): Hosfield, D., Skene, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Design, synthesis and SAR of novel glucokinase activators.

Cheruvallath, Z.S., Gwaltney, S.L., Sabat, M., Tang, M., Feng, J., Wang, H., Miura, J., Guntupalli, P., Jennings, A., Hosfield, D., Lee, B., Wu, Y.

(2013) Bioorg Med Chem Lett 23: 2166-2171

• PubMed: 23434031 
• DOI: https://doi.org/10.1016/j.bmcl.2013.01.093
• Primary Citation Related Structures: 
  4ISE, 4ISF, 4ISG


• PubMed Abstract: 
  

  Guided by co-crystal structures of compounds 15, 22 and 30, an SBDD approach led to the discovery of the 6-methyl pyridone series as a novel class of GKAs that potently activate GK in enzyme and cell assays. Anti-diabetic OGTT efficacy was demonstrated with 54 in a mouse model of type 2 diabetes.

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Organizational Affiliation: 
• Takeda California, 10410 Science Center Drive, San Diego, CA 92121, USA.

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: 52.11 kDa 
• Atom Count: 3,484 
• Modeled Residue Count: 418 
• 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, HXK4 Isoform II 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
1FY	C [auth A]	(2S)-3-cyclohexyl-2-[4-(methylsulfonyl)-2-oxopiperazin-1-yl]-N-(1,3-thiazol-2-yl)propanamide C17 H26 N4 O4 S2 MCVZXAIMSDHSPP-AWEZNQCLSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
IOD	D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.288 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.256	α = 90
b = 78.26	β = 90
c = 120.261	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Hosfield, D., Skene, R.J.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2013-04-03
  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