3DDW

Crystal structure of glycogen phosphorylase complexed with an anthranilimide based inhibitor GSK055


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Anthranilimide based glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Part 3: X-ray crystallographic characterization, core and urea optimization and in vivo efficacy.

Thomson, S.A.Banker, P.Bickett, D.M.Boucheron, J.A.Carter, H.L.Clancy, D.C.Cooper, J.P.Dickerson, S.H.Garrido, D.M.Nolte, R.T.Peat, A.J.Sheckler, L.R.Sparks, S.M.Tavares, F.X.Wang, L.Wang, T.Y.Weiel, J.E.

(2009) Bioorg Med Chem Lett 19: 1177-1182

  • DOI: 10.1016/j.bmcl.2008.12.085
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phen ...

    Key binding interactions of the anthranilimide based glycogen phosphorylase a (GPa) inhibitor 2 from X-ray crystallography studies are described. This series of compounds bind to the AMP site of GP. Using the binding information the core and the phenyl urea moieties were optimized. This work culminated in the identification of compounds with single nanomolar potency as well as in vivo efficacy in a diabetic model.


    Organizational Affiliation

    Metabolic Center for Excellence in Drug Discovery, GlaxoSmithKline, 5 Moore Drive, PO Box 13398, Research Triangle Park, NC 27705, USA. stephen.a.thomson@gsk.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, liver form
A, B
848Homo sapiensMutation(s): 0 
Gene Names: PYGL
EC: 2.4.1.1
Find proteins for P06737 (Homo sapiens)
Go to UniProtKB:  P06737
NIH Common Fund Data Resources
PHAROS  P06737
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
055
Query on 055

Download CCD File 
A, B
(2S)-{[(3-{[(2-chloro-6-methylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]amino}(phenyl)ethanoic acid
C27 H22 Cl N3 O4
KRIVDSIBMDCVLL-DEOSSOPVSA-N
 Ligand Interaction
PLP
Query on PLP

Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
NBG
Query on NBG

Download CCD File 
A, B
1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
 Ligand Interaction
MES
Query on MES

Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CFF
Query on CFF

Download CCD File 
A, B
CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A,B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CFFIC50:  648000   nM  BindingDB
055IC50:  1067   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.368α = 90
b = 124.368β = 90
c = 123.621γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-06-06 
  • Released Date: 2009-01-27 
  • Deposition Author(s): Nolte, R.T.

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance