Human liver glycogen phosphorylase a complexed with caffeine, N-Acetyl-beta-D-glucopyranosylamine, and CP-403700

Experimental Data Snapshot

  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase.

Ekstrom, J.L.Pauly, T.A.Carty, M.D.Soeller, W.C.Culp, J.Danley, D.E.Hoover, D.J.Treadway, J.L.Gibbs, E.M.Fletterick, R.J.Day, Y.S.Myszka, D.G.Rath, V.L.

(2002) Chem Biol 9: 915-924

  • DOI: https://doi.org/10.1016/s1074-5521(02)00186-2
  • Primary Citation of Related Structures:  
    1L5Q, 1L5R, 1L5S, 1L7X

  • PubMed Abstract: 

    Human liver glycogen phosphorylase (HLGP) catalyzes the breakdown of glycogen to maintain serum glucose levels and is a therapeutic target for diabetes. HLGP is regulated by multiple interacting allosteric sites, each of which is a potential drug binding site. We used surface plasmon resonance (SPR) to screen for compounds that bind to the purine allosteric inhibitor site. We determined the affinities of a series of compounds and solved the crystal structures of three representative ligands with K(D) values from 17-550 microM. The crystal structures reveal that the affinities are partly determined by ligand-specific water-mediated hydrogen bonds and side chain movements. These effects could not be predicted; both crystallographic and SPR studies were required to understand the important features of binding and together provide a basis for the design of new allosteric inhibitors targeting this site.

  • Organizational Affiliation

    Exploratory Medicinal Sciences, Groton, CT 06340, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycogen phosphorylase, liver form
A, B
847Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens)
Explore P06737 
Go to UniProtKB:  P06737
GTEx:  ENSG00000100504 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06737
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 700

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
C22 H20 Cl N3 O4
Query on PLP

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
C8 H10 N O6 P
Query on NBG

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
C8 H15 N O6
Query on CFF

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
K [auth B],
L [auth B]
C8 H10 N4 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
700 BindingDB:  1L5Q IC50: 45 (nM) from 1 assay(s)
CFF PDBBind:  1L5Q Kd: 1.08e+5 (nM) from 1 assay(s)
BindingDB:  1L5Q IC50: 6.48e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.713α = 90
b = 124.713β = 90
c = 124.45γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-05-02
    Changes: Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary