3CUV

Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides

• PDB DOI: https://doi.org/10.2210/pdb3CUV/pdb

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


• Deposited: 2008-04-17 Released: 2009-04-21 
• Deposition Author(s): Kyritsi, C., Chrysina, E.D., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.231 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Tracking structure activity relationships of glycogen phosphorylase inhibitors: synthesis, kinetic and crystallographic evaluation of analogues of N-(-D-glucopyranosyl)-N'-oxamides

Czifrak, K., Kyritsi, C., Felfoldi, N., Dosca, T., Gergely, P., Chrysina, E.D., Siafaka-Kapadai, A., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 99.02 kDa 
• Atom Count: 7,580 
• Modelled Residue Count: 812 
• 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
475	B [auth A]	N-[oxo(pyridin-2-ylamino)acetyl]-beta-D-glucopyranosylamine C13 H17 N3 O7 XWDCGBAAIPNJDU-ODYQSLDMSA-N
DMS	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-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
475	BindingDB:  3CUV	Ki: 2.30e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.93 Å
• R-Value Free: 0.231 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.45	α = 90
b = 126.45	β = 90
c = 115.465	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Kyritsi, C., Chrysina, E.D., Leonidas, D.D., Zographos, S.E., Oikonomakos, N.G.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2023-11-15
  Changes: Data collection