2FET

Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. Inhibition of PTP1B. Inhibition of and binding to glycogen phosphorylase in the crystal

• PDB DOI: https://doi.org/10.2210/pdb2FET/pdb

• Classification: TRANSFERASE
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 


• Deposited: 2005-12-16 Released: 2006-12-19 
• Deposition Author(s): Chrysina, E.D., Kosmopoulou, M.N., Leonidas, D.D., Oikonomakos, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.213 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C-D-Glycopyranosylbenzo(hydro)quinones Inhibition of and Binding to Glycogen Phosphorylase in the Crystal

He, L., Zhang, Y.Z., Tanoh, M., Chen, G.-R., Praly, J.-P., Chrysina, E.D., Tiraidis, C., Kosmopoulou, M., Leonidas, D.D., Oikonomakos, N.G.

(2007) European J Org Chem 4: 596-606

• DOI: https://doi.org/10.1002/ejoc.200600548

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 97.81 kDa 
• Atom Count: 6,862 
• Modelled Residue Count: 807 
• 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): 0  EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489  Go to UniProtKB:  P00489

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H53	C [auth A]	(1S)-1,5-anhydro-1-(2,5-dihydroxyphenyl)-D-glucitol C12 H16 O7 QRWWXASRKFWQRP-ZIQFBCGOSA-N
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
H53	BindingDB:  2FET	Ki: 9.00e+5 (nM) from 1 assay(s)
		IC50: 9.77e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.213 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.308	α = 90
b = 128.308	β = 90
c = 116.046	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Chrysina, E.D., Kosmopoulou, M.N., Leonidas, D.D., Oikonomakos, N.G.

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary