2GM9

Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole

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
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This is version 1.4 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. [email protected]


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, muscle form825Oryctolagus cuniculusMutation(s): 0 
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00489
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3TH
Query on 3TH
Download Ideal Coordinates CCD File 
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
Query on PLR
Download Ideal Coordinates CCD File 
B [auth A](5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE
C8 H12 N O5 P
RBCOYOYDYNXAFA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding 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 = 126.781α = 90
b = 126.781β = 90
c = 115.144γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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