3DD1

Crystal structure of glycogen phophorylase complexed with an anthranilimide based inhibitor GSK254


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 

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
  • Primary Citation of Related Structures:  

  • 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 Gene View: PYGL
Go to UniProtKB:  P06737
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

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Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PLP
Query on PLP

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Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
CFF
Query on CFF

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Download CCD File 
A, B
CAFFEINE
3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
 Ligand Interaction
NBG
Query on NBG

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

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Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
25D
Query on 25D

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Download CCD File 
A, B
2-cyclohexyl-N-[(3-{[(2,4,6-trimethylphenyl)carbamoyl]amino}naphthalen-2-yl)carbonyl]-D-alanine
C30 H35 N3 O4
ZYHGLTOSKWXGQM-PMERELPUSA-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 (94) BINDINGDB
25DIC50: 10 - 350 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 124.103α = 90.00
b = 124.103β = 90.00
c = 123.222γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
HKL-2000data reduction
ADSCdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-06-04 
  • Released Date: 2009-04-21 
  • Deposition Author(s): Nolte, R.T.

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance