1Z6P

Glycogen phosphorylase AMP site inhibitor complex

• PDB DOI:  https://doi.org/10.2210/pdb1Z6P/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): Yes 


• Deposited: 2005-03-23 Released: 2005-04-12 
• Deposition Author(s): Kristiansen, M., Andersen, B., Iversen, L.F., Westergaard, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.260 
• R-Value Work: 0.200 

Literature

Identification, synthesis and chracterization of new glycogen phosphorylase inhibitors binding to the allosteric AMP site

Kristiansen, M., Andersen, B., Iversen, L.F., Westergaard, N.

(2004) J Med Chem 47: 3537-3545

• PubMed: 15214781 
• DOI: https://doi.org/10.1021/jm031121n
• Primary Citation of Related Structures:  
  1Z6P, 1Z6Q


• PubMed Abstract: 
  

  Inhibition of glycogen phosphorylase (GP) has attracted considerable attention during the last five to 10 years as a means of treating the elevated hepatic glucose production seen in patients with type 2 diabetes. Several different GP inhibitors binding to various binding sites of the GP enzyme have been reported in the literature. In this paper we report on a novel class of compounds that have been identified as potent GP inhibitors. Their synthesis, mode of binding to the allosteric AMP site as well as in vitro data on GP inhibition are shown. The most potent inhibitor was found to be 4-[2,4-bis-(3-nitrobenzoylamino)phenoxy]phthalic acid (4j) with an IC(50) value of 74 nM. This compound together with a closely related analogue was further characterized by enzyme kinetics and in primary rat hepatocytes.

---

Organizational Affiliation: 

Novo Nordisk A/S, Novo Nordisk Park, DK-2760 Måløv, Denmark. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 97.94 kDa 
• Atom Count: 6,794 
• Modelled Residue Count: 813 
• Deposited Residue Count: 842 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	842	Oryctolagus cuniculus	Mutation(s): 1  Gene Names: PYGM EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
194	B [auth A]	4-{2-[(3-NITROBENZOYL)AMINO]PHENOXY}PHTHALIC ACID C21 H14 N2 O8 NAQUAVBNIYTIIS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Binding Affinity Annotations
ID	Source	Binding Affinity
194	BindingDB:  1Z6P	IC50: 900 (nM) from 1 assay(s)
	PDBBind:  1Z6P	IC50: 900 (nM) from 1 assay(s)
	Binding MOAD:  1Z6P	IC50: 900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.260 
• R-Value Work: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.47	α = 90
b = 127.47	β = 90
c = 115.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
X-PLOR	model building
X-PLOR	refinement
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-12 
Deposition Author(s): Kristiansen, M., Andersen, B., Iversen, L.F., Westergaard, N.

Revision History  

• Version 1.0: 2005-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance