6R0H | pdb_00006r0h

Glycogen Phosphorylase b in complex with 3

• PDB DOI: https://doi.org/10.2210/pdb6R0H/pdb

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


• Deposited: 2019-03-13 Released: 2019-04-10 
• Deposition Author(s): Tsagkarakou, S.A., Koulas, M.S., Kyriakis, E., Stravodimos, G.A., Skamnaki, V.T., Leonidas, D.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors.

Fischer, T., Koulas, S.M., Tsagkarakou, A.S., Kyriakis, E., Stravodimos, G.A., Skamnaki, V.T., Liggri, P.G.V., Zographos, S.E., Riedl, R., Leonidas, D.D.

(2019) Molecules 24

• PubMed: 30987252 
• DOI: https://doi.org/10.3390/molecules24071322
• Primary Citation Related Structures: 
  6R0H, 6R0I


• PubMed Abstract: 
  

  Structure-based design and synthesis of two biphenyl- N -acyl-β-d-glucopyranosylamine derivatives as well as their assessment as inhibitors of human liver glycogen phosphorylase (hlGPa, a pharmaceutical target for type 2 diabetes) is presented. X-ray crystallography revealed the importance of structural water molecules and that the inhibitory efficacy correlates with the degree of disturbance caused by the inhibitor binding to a loop crucial for the catalytic mechanism. The in silico-derived models of the binding mode generated during the design process corresponded very well with the crystallographic data.

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Organizational Affiliation: 
• Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [e-mail].
Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece. [e-mail].
Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue, 11635 Athens, Greece. [e-mail].
Institute of Chemistry and Biotechnology, Center of Organic and Medicinal Chemistry, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland. [e-mail].
Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. [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 (software)

Biological Assembly Evidence: equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 98.05 kDa 
• Atom Count: 6,845 
• Modeled Residue Count: 810 
• Deposited Residue Count: 843 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	843	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
JN2	B [auth A]	3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide C19 H20 F N O6 ZNFXGMNTWYBCJQ-OGJJZOIMSA-N
PLP	C [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.287	α = 90
b = 128.287	β = 90
c = 116.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Tsagkarakou, S.A., Koulas, M.S., Kyriakis, E., Stravodimos, G.A., Skamnaki, V.T., Leonidas, D.D.

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-04-24
  Changes: Data collection, Database references
• Version 1.2: 2025-04-09
  Changes: Data collection, Database references, Structure summary