2Y5L

orally active aminopyridines as inhibitors of tetrameric fructose 1,6- bisphosphatase

• PDB DOI: https://doi.org/10.2210/pdb2Y5L/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-01-14 Released: 2011-05-18 
• Deposition Author(s): ruf, a., hebeisen, p., haap, w., kuhn, b., mohr, p., wessel, h.p., zutter, u., kirchner, s., benz, j., joseph, c., alvarez-sanchez, r., gubler, m., schott, b., benardeau, a., tozzo, e., kitas, e.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Orally Active Aminopyridines as Inhibitors of Tetrameric Fructose-1,6-Bisphosphatase.

Hebeisen, P., Haap, W., Kuhn, B., Mohr, P., Wessel, H.P., Zutter, U., Kirchner, S., Ruf, A., Benz, J., Joseph, C., Alvarez-Sanchez, R., Gubler, M., Schott, B., Benardeau, A., Tozzo, E., Kitas, E.

(2011) Bioorg Med Chem Lett 21: 3237

• PubMed: 21550236 
• DOI: https://doi.org/10.1016/j.bmcl.2011.04.044
• Primary Citation of Related Structures:  
  2Y5K, 2Y5L


• PubMed Abstract: 
  

  A novel sulfonylureido pyridine series exemplified by compound 19 yielded potent inhibitors of FBPase showing significant glucose reduction and modest glycogen lowering in the acute db/db mouse model for Type-2 diabetes. Our inhibitors occupy the allosteric binding site and also extend into the dyad interface region of tetrameric FBPase.

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Organizational Affiliation: 

F. Hoffmann-La Roche Ltd, Discovery Research Basel, CH-4070 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 298.05 kDa 
• Atom Count: 20,167 
• Modelled Residue Count: 2,548 
• Deposited Residue Count: 2,704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FRUCTOSE-1,6-BISPHOSPHATASE 1	A, B, C, D, E, F, G, H	338	Homo sapiens	Mutation(s): 1  EC: 3.1.3.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09467 (Homo sapiens) Explore P09467  Go to UniProtKB:  P09467
GTEx:  ENSG00000165140

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RO8	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	N-{[(2Z)-5-bromo-1,3-thiazol-2(3H)-ylidene]carbamoyl}-3-chlorobenzenesulfonamide C10 H7 Br Cl N3 O3 S2 VRHXEPNJEQXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RO8	PDBBind:  2Y5L	IC50: 330 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.791	α = 90
b = 285.084	β = 97.3
c = 83.687	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): ruf, a., hebeisen, p., haap, w., kuhn, b., mohr, p., wessel, h.p., zutter, u., kirchner, s., benz, j., joseph, c., alvarez-sanchez, r., gubler, m., schott, b., benardeau, a., tozzo, e., kitas, e.

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-05-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description