2IEI

Crystal structure of rabbit muscle glycogen phosphorylase in complex with 3,4-dihydro-2-quinolone

• PDB DOI: https://doi.org/10.2210/pdb2IEI/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2006-09-19 Released: 2006-12-26 
• Deposition Author(s): Birch, A.M., Kenny, P.W., Oikonomakos, N.G., Otterbein, L., Schofield, P., Whittamore, P.R.O., Whalley, D.P., Rowsell, S., Pauptit, R., Pannifer, A., Breed, J., Minshull, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free: 
  0.297 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.268 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Development of potent, orally active 1-substituted-3,4-dihydro-2-quinolone glycogen phosphorylase inhibitors.

Birch, A.M., Kenny, P.W., Oikonomakos, N.G., Otterbein, L., Schofield, P., Whittamore, P.R., Whalley, D.P.

(2007) Bioorg Med Chem Lett 17: 394-399

• PubMed: 17095214 
• DOI: https://doi.org/10.1016/j.bmcl.2006.10.037
• Primary Citation of Related Structures:  
  2IEG, 2IEI


• PubMed Abstract: 
  

  A series of substituted 3,4-dihydro-2-quinolone glycogen phosphorylase inhibitors, which have potential as antidiabetic agents, is described. Initial members of the series showed good enzyme inhibitory potency but poor physical properties. Optimisation of the 1-substituent led to 2,3-dihydroxypropyl compounds which showed good in vitro potency and improved physical properties, together with good DMPK profiles and acute in vivo efficacy in a rat model. X-ray crystallographic data are presented, showing an unexpected variety of binding orientations at the dimer interface site.

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Organizational Affiliation: 

AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 195.94 kDa 
• Atom Count: 13,536 
• Modelled Residue Count: 1,590 
• Deposited Residue Count: 1,684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A, B	842	Oryctolagus cuniculus	Mutation(s): 0  EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRX	D [auth A], F [auth B]	(S)-2-CHLORO-N-(1-(2-(2-HYDROXYETHYLAMINO)-2-OXOETHYL)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL)-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE C20 H19 Cl N4 O4 S VUKPNWLGSLOHIF-AWEZNQCLSA-N
PLR	C [auth A], E [auth B]	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE C8 H12 N O5 P RBCOYOYDYNXAFA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.91 Å
• R-Value Free:  0.297 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.268 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.402	α = 90
b = 125.344	β = 90
c = 129.309	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Birch, A.M., Kenny, P.W., Oikonomakos, N.G., Otterbein, L., Schofield, P., Whittamore, P.R.O., Whalley, D.P., Rowsell, S., Pauptit, R., Pannifer, A., Breed, J., Minshull, C.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary