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 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    1E1Y, 1GFZ, 1C8K

  • 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 phosphorylase (GP) and to cause glycogen accumulation in A549 non-small cell lung carcinoma cells (Kaiser, A ...

    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cell lung carcinoma cells (Kaiser, A., Nishi, K., Gorin, F.A., Walsh, D.A., Bradbury, E. M., and Schnier, J. B., unpublished data).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: 
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLYCOGEN PHOSPHORYLASE, MUSCLE FORMA842Oryctolagus cuniculusMutation(s): 0 
Gene Names: PYGM
EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus)
Explore P00489 
Go to UniProtKB:  P00489
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPB (Subject of Investigation/LOI)
Query on CPB

Download Ideal Coordinates CCD File 
B [auth A]2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE
C21 H20 Cl N O5
BIIVYFLTOXDAOV-YVEFUNNKSA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
GLC (Subject of Investigation/LOI)
Query on GLC

Download Ideal Coordinates CCD File 
D [auth A]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
PO3
Query on PO3

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CPB BindingDB:  1E1Y IC50: min: 1000, max: 1200 (nM) from 2 assay(s)
Binding MOAD:  1E1Y IC50: 2500 (nM) from 1 assay(s)
PDBBind:  1E1Y IC50: 2500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.759α = 90
b = 126.759β = 90
c = 116.018γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-17
    Type: Initial release
  • Version 1.1: 2011-08-31
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-05-22
    Changes: Data collection, Derived calculations, Other, Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary