Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 195.82 kDa 
• Atom Count: 13701 
• Modelled Residue Count: 1582 
• Deposited Residue Count: 1692 
• Unique protein chains: 1

2ATI

Glycogen Phosphorylase Inhibitors

• DOI: 10.2210/pdb2ATI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-08-25 Released: 2006-08-25 
• Deposition Author(s): Klabunde, T., Wendt, K.U., Kadereit, D., Brachvogel, V., Burger, H.J., Herling, A.W., Oikonomakos, N.G., Schmoll, D., Sarubbi, E., von Roedern, E., Schoenafinger, K., Defossa, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Acyl ureas as human liver glycogen phosphorylase inhibitors for the treatment of type 2 diabetes.

Klabunde, T., Wendt, K.U., Kadereit, D., Brachvogel, V., Burger, H.J., Herling, A.W., Oikonomakos, N.G., Kosmopoulou, M.N., Schmoll, D., Sarubbi, E., von Roedern, E., Defossa, E.

(2005) J Med Chem 48: 6178-6193

• PubMed: 16190745 
• DOI: 10.1021/jm049034y
• Primary Citation of Related Structures:  
  2ATI


• PubMed Abstract: 
  

Using a focused screening approach, acyl ureas have been discovered as a new class of inhibitors of human liver glycogen phosphorylase (hlGPa). The X-ray structure of screening hit 1 (IC50 = 2 microM) in a complex with rabbit muscle glycogen phosphorylase b reveals that 1 binds at the AMP site, the main allosteric effector site of the dimeric enzyme. A first cycle of chemical optimization supported by X-ray structural data yielded derivative 21, which inhibited hlGPa with an IC50 of 23 +/- 1 nM, but showed only moderate cellular activity in isolated rat hepatocytes (IC50 = 6.2 microM). Further optimization was guided by (i) a 3D pharmacophore model that was derived from a training set of 24 compounds and revealed the key chemical features for the biological activity and (ii) the 1.9 angstroms crystal structure of 21 in complex with hlGPa. A second set of compounds was synthesized and led to 42 with improved cellular activity (hlGPa IC50 = 53 +/- 1 nM; hepatocyte IC50 = 380 nM). Administration of 42 to anaesthetized Wistar rats caused a significant reduction of the glucagon-induced hyperglycemic peak. These findings are consistent with the inhibition of hepatic glycogenolysis and support the use of acyl ureas for the treatment of type 2 diabetes.

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Related Citations: 

• Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs
  Oikonomakos, N.G., Kosmopoulou, M.N., Chrysina, E.D., Leonidas, D.D., Kostas, I.D., Wendt, K.U., Klabunde, T., Defossa, E.
  (2005) Protein Sci 14: 1760

• Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
  Rath, V.L., Ammirati, M., LeMotte, P.K., Fennell, K.F., Mansour, M.N., Danley, D.E., Hynes, T.R., Schulte, G.K., Wasilko, D.J., Pandit, J.
  (2000) Mol Cell 6: 139

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Organizational Affiliation: 

Sanofi-Aventis Deutschland GmbH, Scientific and Medical Affairs, D-65926 Frankfurt am Main, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, liver form	A, B	846	Homo sapiens	Mutation(s): 0  Gene Names: PYGL EC: 2.4.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P06737 (Homo sapiens) Explore P06737  Go to UniProtKB:  P06737
PHAROS:  P06737 GTEx:  ENSG00000100504

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHU (Subject of Investigation/LOI)	D [auth A], G [auth B]	N-(2-CHLORO-4-FLUOROBENZOYL)-N'-(5-HYDROXY-2-METHOXYPHENYL)UREA C15 H12 Cl F N2 O4 RFOBTYLRURSVJE-UHFFFAOYSA-N
PLP (Subject of Investigation/LOI)	E [auth A], H [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
GLC (Subject of Investigation/LOI)	C [auth A], F [auth B]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IHU	BindingDB:  2ATI	IC50: min: 22.91, max: 23 (nM) from 2 assay(s)
	Binding MOAD:  2ATI	IC50: 23 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.5	α = 90
b = 124.5	β = 90
c = 123.2	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
XDS	data reduction
AMoRE	phasing
CNX	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-08-25 
• Released Date: 2006-08-25 
Deposition Author(s): Klabunde, T., Wendt, K.U., Kadereit, D., Brachvogel, V., Burger, H.J., Herling, A.W., Oikonomakos, N.G., Schmoll, D., Sarubbi, E., von Roedern, E., Schoenafinger, K., Defossa, E.

Revision History  

• Version 1.0: 2006-08-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary