4IXC | pdb_00004ixc

Crystal structure of Human Glucokinase in complex with a small molecule activator.

• PDB DOI: https://doi.org/10.2210/pdb4IXC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-01-25 Released: 2013-04-24 
• Deposition Author(s): Ogg, D.J., Hargreaves, D., Gerhardt, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Matched triplicate design sets in the optimisation of glucokinase activators maximising medicinal chemistry information content

Waring, M.J., Bennett, S.N.L., Boyd, S., Campbell, L., Davies, R.D.M., Gerhardt, S., Hargreaves, D., G Martin, N., Robb, G.R., Wilkinson, G.

To be published.

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: 51.48 kDa 
• Atom Count: 3,755 
• Modeled Residue Count: 443 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase isoform 3	A	456	Homo sapiens	Mutation(s): 4  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
1JD	D [auth A]	(2S)-2-{[1-(3-chloropyridin-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-yl]oxy}-N-(5-methylpyridin-2-yl)-3-(propan-2-yloxy)propanamide C22 H22 Cl N7 O3 AAGISEXHOPCAHZ-KRWDZBQOSA-N
GLC	C [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.249 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.628	α = 90
b = 77.628	β = 90
c = 85.824	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Ogg, D.J., Hargreaves, D., Gerhardt, S.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Structure summary