1EXV

HUMAN LIVER GLYCOGEN PHOSPHORYLASE A COMPLEXED WITH GLCNAC AND CP-403,700


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 

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: 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 ...

    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.


    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LIVER GLYCOGEN PHOSPHORYLASEA, B847Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
700 (Subject of Investigation/LOI)
Query on 700

Download Ideal Coordinates CCD File 
E [auth A], I [auth B][5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID
C22 H20 Cl N3 O4
RONLONYAIBUEKT-IBGZPJMESA-N
 Ligand Interaction
PLP (Subject of Investigation/LOI)
Query on PLP

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

Download Ideal Coordinates CCD File 
F [auth A], J [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
700 BindingDB:  1EXV IC50: 45 (nM) from 1 assay(s)
Binding MOAD:  1EXV IC50: 45 (nM) from 1 assay(s)
PDBBind:  1EXV IC50: 45 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.236 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.629α = 90
b = 124.629β = 90
c = 124.064γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

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