2ATI

Glycogen Phosphorylase Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Acyl ureas as human liver glycogen phosphorylase inhibitors for the treatment of type 2 diabetes.

Klabunde, T.Wendt, K.U.Kadereit, D.Brachvogel, V.Burger, H.J.Herling, A.W.Oikonomakos, N.G.Kosmopoulou, M.N.Schmoll, D.Sarubbi, E.von Roedern, E.Defossa, E.

(2005) J Med Chem 48: 6178-6193

  • DOI: 10.1021/jm049034y
  • Primary Citation of Related Structures:  
    2ATI

  • PubMed Abstract: 
  • Using a focused screening approach, acyl ureas have been discovered as a new class of inhibitors of human liver glycogen phosphorylase (hlGPa). The X-ray structure of screening hit 1 (IC50 = 2 microM) in a complex with rabbit muscle glycogen phosphorylase b reveals that 1 binds at the AMP site, the main allosteric effector site of the dimeric enzyme ...

    Using a focused screening approach, acyl ureas have been discovered as a new class of inhibitors of human liver glycogen phosphorylase (hlGPa). The X-ray structure of screening hit 1 (IC50 = 2 microM) in a complex with rabbit muscle glycogen phosphorylase b reveals that 1 binds at the AMP site, the main allosteric effector site of the dimeric enzyme. A first cycle of chemical optimization supported by X-ray structural data yielded derivative 21, which inhibited hlGPa with an IC50 of 23 +/- 1 nM, but showed only moderate cellular activity in isolated rat hepatocytes (IC50 = 6.2 microM). Further optimization was guided by (i) a 3D pharmacophore model that was derived from a training set of 24 compounds and revealed the key chemical features for the biological activity and (ii) the 1.9 angstroms crystal structure of 21 in complex with hlGPa. A second set of compounds was synthesized and led to 42 with improved cellular activity (hlGPa IC50 = 53 +/- 1 nM; hepatocyte IC50 = 380 nM). Administration of 42 to anaesthetized Wistar rats caused a significant reduction of the glucagon-induced hyperglycemic peak. These findings are consistent with the inhibition of hepatic glycogenolysis and support the use of acyl ureas for the treatment of type 2 diabetes.


    Related Citations: 
    • Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs
      Oikonomakos, N.G., Kosmopoulou, M.N., Chrysina, E.D., Leonidas, D.D., Kostas, I.D., Wendt, K.U., Klabunde, T., Defossa, E.
      (2005) Protein Sci 14: 1760
    • Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
      Rath, V.L., Ammirati, M., LeMotte, P.K., Fennell, K.F., Mansour, M.N., Danley, D.E., Hynes, T.R., Schulte, G.K., Wasilko, D.J., Pandit, J.
      (2000) Mol Cell 6: 139

    Organizational Affiliation

    Sanofi-Aventis Deutschland GmbH, Scientific and Medical Affairs, D-65926 Frankfurt am Main, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, liver formA, B846Homo sapiensMutation(s): 0 
Gene Names: PYGL
EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens)
Explore P06737 
Go to UniProtKB:  P06737
PHAROS:  P06737
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHU (Subject of Investigation/LOI)
Query on IHU

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]N-(2-CHLORO-4-FLUOROBENZOYL)-N'-(5-HYDROXY-2-METHOXYPHENYL)UREA
C15 H12 Cl F N2 O4
RFOBTYLRURSVJE-UHFFFAOYSA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]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 
C [auth A], F [auth B]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IHU BindingDB:  2ATI IC50: min: 22.91, max: 23 (nM) from 2 assay(s)
Binding MOAD:  2ATI IC50: 23 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.5α = 90
b = 124.5β = 90
c = 123.2γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
XDSdata reduction
AMoREphasing
CNXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary