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


Ligand Structure Quality Assessment 


This is version 1.2 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:  
    3DD1, 3DDS, 3DDW

  • 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 phenyl urea moieties were optimized ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycogen phosphorylase, liver formA, B848Homo 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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
055 (Subject of Investigation/LOI)
Query on 055

Download Ideal Coordinates CCD File 
F [auth A], M [auth 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 (Subject of Investigation/LOI)
Query on PLP

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

Download Ideal Coordinates CCD File 
C [auth A], H [auth B]N-acetyl-beta-D-glucopyranosylamine
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
K [auth B], L [auth B]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
CFF (Subject of Investigation/LOI)
Query on CFF

Download Ideal Coordinates CCD File 
E [auth A], J [auth B]CAFFEINE
C8 H10 N4 O2
RYYVLZVUVIJVGH-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
G [auth A], N [auth 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, BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
CFF BindingDB:  3DDW IC50: 6.48e+5 (nM) from 1 assay(s)
055 Binding MOAD:  3DDW IC50: 1067 (nM) from 1 assay(s)
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



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary