1E1Y

Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Flavopiridol Inhibits Glycogen Phosphorylase by Binding at the Inhibitor Site

Oikonomakos, N.G.Schnier, J.B.Zographos, S.E.Skamnaki, V.T.Tsitsanou, K.E.Johnson, L.N.

(2000) J.Biol.Chem. 275: 34566

  • DOI: 10.1074/jbc.M004485200
  • Primary Citation of Related Structures:  1C8K, 1GFZ

  • PubMed Abstract: 
  • Flavopiridol (L86-8275) ((-)-cis-5, 7-dihydroxy-2-(2-chlorophenyl)-8-[4-(3-hydroxy-1-methyl)-piperidinyl] -4H-benzopyran-4-one), a potential antitumor drug, currently in phase II trials, has been shown to be an inhibitor of muscle glycogen phosphoryl ...

    Flavopiridol (L86-8275) ((-)-cis-5, 7-dihydroxy-2-(2-chlorophenyl)-8-[4-(3-hydroxy-1-methyl)-piperidinyl] -4H-benzopyran-4-one), a potential antitumor drug, currently in phase II trials, has been shown to be an inhibitor of muscle glycogen phosphorylase (GP) and to cause glycogen accumulation in A549 non-small cell lung carcinoma cells (Kaiser, A., Nishi, K., Gorin, F.A., Walsh, D.A., Bradbury, E. M., and Schnier, J. B., unpublished data). Kinetic experiments reported here show that flavopiridol inhibits GPb with an IC(50) = 15.5 microm. The inhibition is synergistic with glucose resulting in a reduction of IC(50) for flavopiridol to 2.3 microm and mimics the inhibition of caffeine. In order to elucidate the structural basis of inhibition, we determined the structures of GPb complexed with flavopiridol, GPb complexed with caffeine, and GPa complexed with both glucose and flavopiridol at 1.76-, 2.30-, and 2.23-A resolution, and refined to crystallographic R values of 0.216 (R(free) = 0.247), 0.189 (R(free) = 0.219), and 0.195 (R(free) = 0.252), respectively. The structures provide a rational for flavopiridol potency and synergism with glucose inhibitory action. Flavopiridol binds at the allosteric inhibitor site, situated at the entrance to the catalytic site, the site where caffeine binds. Flavopiridol intercalates between the two aromatic rings of Phe(285) and Tyr(613). Both flavopiridol and glucose promote the less active T-state through localization of the closed position of the 280s loop which blocks access to the catalytic site, thereby explaining their synergistic inhibition. The mode of interactions of flavopiridol with GP is different from that of des-chloro-flavopiridol with CDK2, illustrating how different functional parts of the inhibitor can be used to provide specific and potent binding to two different enzymes.


    Related Citations: 
    • The Structure of Glycogen Phosphorylase B with an Alkyl-Dihydropyridine-Dicarboxylic Acid Compound, a Novel and Potent Inhibitor
      Zographos, S.E.,Oikonomakos, N.G.,Tsitsanou, K.E.,Leonidas, D.D.,Chrysina, E.D.,Skamnaki, V.T.,Bischoff, H.,Goldman, S.,Schramm, M.,Watson, K.A.,Johnson, L.N.
      (1997) Structure 5: 1413
    • Allosteric Inhibition of Glycogen Phosphorylase a by the Potential Antidiabetic Drug 3-Isopropyl 4-(2-Chlorophenyl)-1,4-Dihydro-1-Ethyl-2-Methyl-Pyridine-3,5,6-Tricarboxylate
      Oikonomakos, N.G.,Tsitsanou, K.E.,Zographos, S.E.,Skamnaki, V.T.,Goldmann, S.,Bischoff, H.
      (1999) Protein Sci. 8: 1930


    Organizational Affiliation

    Institute of Biological Research and Biotechnology, The National Hellenic Research Foundation, 48 Vas. Constantinou Avenue, Athens 11635, Greece. ngo@eie.gr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
A
842Oryctolagus cuniculusGene Names: PYGM
EC: 2.4.1.1
Find proteins for P00489 (Oryctolagus cuniculus)
Go to Gene View: PYGM
Go to UniProtKB:  P00489
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download SDF File 
Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
CPB
Query on CPB

Download SDF File 
Download CCD File 
A
2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE
FLAVOPIRIDOL
C21 H20 Cl N O5
BIIVYFLTOXDAOV-YVEFUNNKSA-N
 Ligand Interaction
PO3
Query on PO3

Download SDF File 
Download CCD File 
A
PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 126.759α = 90.00
b = 126.759β = 90.00
c = 116.018γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-17
    Type: Initial release
  • Version 1.1: 2011-08-31
    Type: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance