4L3Q | pdb_00004l3q

Crystal structure of glucokinase-activator complex

• PDB DOI: https://doi.org/10.2210/pdb4L3Q/pdb

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


• Deposited: 2013-06-06 Released: 2013-07-24 
• Deposition Author(s): Gajiwala, K.S., Filipski, K.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.304 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

Pyrimidone-based series of glucokinase activators with alternative donor-acceptor motif.

Filipski, K.J., Guzman-Perez, A., Bian, J., Perreault, C., Aspnes, G.E., Didiuk, M.T., Dow, R.L., Hank, R.F., Jones, C.S., Maguire, R.J., Tu, M., Zeng, D., Liu, S., Knafels, J.D., Litchfield, J., Atkinson, K., Derksen, D.R., Bourbonais, F., Gajiwala, K.S., Hickey, M., Johnson, T.O., Humphries, P.S., Pfefferkorn, J.A.

(2013) Bioorg Med Chem Lett 23: 4571-4578

• PubMed: 23831135 
• DOI: https://doi.org/10.1016/j.bmcl.2013.06.036
• Primary Citation Related Structures: 
  4L3Q


• PubMed Abstract: 
  

  Glucokinase activators are a class of experimental agents under investigation as a therapy for Type 2 diabetes mellitus. An X-ray crystal structure of a modestly potent agent revealed the potential to substitute the common heterocyclic amide donor-acceptor motif for a pyridone moiety. We have successfully demonstrated that both pyridone and pyrimidone heterocycles can be used as a potent donor-acceptor substituent. Several sub-micromolar analogs that possess the desired partial activator profile were synthesized and characterized. Unfortunately, the most potent activators suffered from sub-optimal pharmacokinetic properties. Nonetheless, these donor-acceptor motifs may find utility in other glucokinase activator series or beyond.

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Organizational Affiliation: 
• Cardiovascular, Metabolic, and Endocrine Diseases Chemistry, Pfizer Worldwide Research and Development, 620 Memorial Dr, Cambridge, MA 02139, USA. [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: 51.63 kDa 
• Atom Count: 3,537 
• Modeled Residue Count: 447 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	457	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
926	C [auth A]	6-{3-[(1-methyl-1H-imidazol-2-yl)sulfanyl]phenyl}pyridin-2(1H)-one C15 H13 N3 O S YYWBGPHQPMDZEM-UHFFFAOYSA-N
GLC	B [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
926	BindingDB:  4L3Q	EC50: 2000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.304 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.512	α = 90
b = 79.512	β = 90
c = 321.131	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Gajiwala, K.S., Filipski, K.J.

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2013-08-07
  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: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary