1L7X

Human liver glycogen phosphorylase b complexed with caffeine, N-acetyl-beta-D-glucopyranosylamine, and CP-403,700


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  1L5Q, 1L5R, 1L5S

  • 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 bin ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycogen phosphorylase, liver form
A, B
847Homo sapiensGene 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
700
Query on 700

Download SDF File 
Download CCD File 
A, B
[5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID
CP403700, (S)-1-{2-[(5-CHLORO-1H-INDOLE-2-CARBONYL)-AMINO]-3-PHENYL-PROPIONYL}-AZETIDINE-3-CARBOXYLATE
C22 H20 Cl N3 O4
RONLONYAIBUEKT-IBGZPJMESA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
B
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-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

Download SDF File 
Download CCD File 
A, B
1-N-ACETYL-BETA-D-GLUCOSAMINE
C8 H15 N O6
IBONACLSSOLHFU-JAJWTYFOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.206 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 124.072α = 90.00
b = 124.072β = 90.00
c = 122.849γ = 120.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance