1EM6

HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-526,423


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Human liver glycogen phosphorylase inhibitors bind at a new allosteric site.

Rath, V.L.Ammirati, M.Danley, D.E.Ekstrom, J.L.Gibbs, E.M.Hynes, T.R.Mathiowetz, A.M.McPherson, R.K.Olson, T.V.Treadway, J.L.Hoover, D.J.

(2000) Chem Biol 7: 677-682

  • DOI: https://doi.org/10.1016/s1074-5521(00)00004-1
  • Primary Citation of Related Structures:  
    1EM6, 1EXV

  • PubMed Abstract: 

    Glycogen phosphorylases catalyze the breakdown of glycogen to glucose-1-phosphate for glycolysis. Maintaining control of blood glucose levels is critical in minimizing the debilitating effects of diabetes, making liver glycogen phosphorylase a potential therapeutic target. The binding site in human liver glycogen phosphorylase (HLGP) for a class of promising antidiabetic agents was identified crystallographically. The site is novel and functions allosterically by stabilizing the inactive conformation of HLGP. The initial view of the complex revealed key structural information and inspired the design of a new class of inhibitors which bind with nanomolar affinity and whose crystal structure is also described. We have identified the binding site of a new class of allosteric HLGP inhibitors. The crystal structure revealed the details of inhibitor binding, led to the design of a new class of compounds, and should accelerate efforts to develop therapeutically relevant molecules for the treatment of diabetes.


  • Organizational Affiliation

    Department of Exploratory Medicinal Sciences, Global Research and Development, Pfizer Inc., Groton, CT 06340, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LIVER GLYCOGEN PHOSPHORYLASE
A, B
847Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000100504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06737
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CP4
Query on CP4

Download Ideal Coordinates CCD File 
D [auth A]BIS[5-CHLORO-1H-INDOL-2-YL-CARBONYL-AMINOETHYL]-ETHYLENE GLYCOL
C24 H24 Cl2 N4 O4
MWWXABBBAPKJDX-UHFFFAOYSA-N
PLP
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
NBG
Query on NBG

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

Download Ideal Coordinates CCD File 
H [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CP4 PDBBind:  1EM6 IC50: 6 (nM) from 1 assay(s)
BindingDB:  1EM6 IC50: min: 6, max: 6 (nM) from 2 assay(s)
Binding MOAD:  1EM6 IC50: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.314α = 90
b = 123.314β = 90
c = 122.319γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: Advisory, Data collection, Derived calculations, Structure summary