2GM9

Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole

• PDB DOI: https://doi.org/10.2210/pdb2GM9/pdb

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


• Deposited: 2006-04-06 Released: 2007-02-13 
• Deposition Author(s): Otterbein, L.R., Pannifer, A.D., Tucker, J., Breed, J., Oikonomakos, N.G., Minshull, C., Rowsell, S., Pauptit, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.245 
• R-Value Work: 0.182 
• R-Value Observed: 0.186 

Starting Model: other

Literature

Novel thienopyrrole glycogen phosphorylase inhibitors: synthesis, in vitro SAR and crystallographic studies.

Whittamore, P.R., Addie, M.S., Bennett, S.N., Birch, A.M., Butters, M., Godfrey, L., Kenny, P.W., Morley, A.D., Murray, P.M., Oikonomakos, N.G., Otterbein, L.R., Pannifer, A.D., Parker, J.S., Readman, K., Siedlecki, P.S., Schofield, P., Stocker, A., Taylor, M.J., Townsend, L.A., Whalley, D.P., Whitehouse, J.

(2006) Bioorg Med Chem Lett 16: 5567-5571

• PubMed: 16945526 
• DOI: https://doi.org/10.1016/j.bmcl.2006.08.047
• Primary Citation of Related Structures:  
  2GJ4, 2GM9


• PubMed Abstract: 
  

  Two series of novel thienopyrrole inhibitors of recombinant human liver glycogen phosphorylase a (GPa) which are effective in reducing glucose output from rat hepatocytes are described. Representative compounds have been shown to bind at the dimer interface site of the rabbit muscle enzyme by X-ray crystallography.

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Organizational Affiliation: 

AstraZeneca, 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,PQS (software)

Macromolecule Content

• Total Structure Weight: 95.86 kDa 
• Atom Count: 7,052 
• Modelled Residue Count: 805 
• Deposited Residue Count: 825 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	825	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
3TH	C [auth A]	2-CHLORO-N-[(3R)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE C16 H12 Cl N3 O2 S LJAHIGGEXIWVJG-LLVKDONJSA-N
PLR	B [auth A]	(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE C8 H12 N O5 P RBCOYOYDYNXAFA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3TH	PDBBind:  2GM9	IC50: 41 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.245 
• R-Value Work: 0.182 
• R-Value Observed: 0.186 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.781	α = 90
b = 126.781	β = 90
c = 115.144	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): Otterbein, L.R., Pannifer, A.D., Tucker, J., Breed, J., Oikonomakos, N.G., Minshull, C., Rowsell, S., Pauptit, R.A.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description