2CN0

Complex of Recombinant Human Thrombin with a Designed Inhibitor

Summary for 2CN0

• Entry DOI: 10.2210/pdb2cn0/pdb
• Related PRD ID: PRD_000481
• Descriptor: PROTHROMBIN PRECURSOR, HIRUDIN IIA, 4-(1R,3AS,4R,8AS,8BR)-[1-DIFLUOROMETHYL-2-(4-FLUOROBENZYL)-3-OXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZAMIDINE, ... (7 entities in total)
• Functional Keywords: acute phase, blood coagulation, calcium-binding, glycoprotein, hydrolase, serine protease, serine protease inhibitor complex, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: HOMO SAPIENS (HUMAN); More
• Cellular location: Secreted, extracellular space: P00734 P00734; Secreted: P28503
• Total number of polymer chains: 3
• Total formula weight: 34801.78

Authors

Hoffmann-Roder, A.,Schweizer, E.,Egger, J.,Seiler, P.,Obst-Sander, U.,Wagner, B.,Kansy, M.,Banner, D.W.,Diederich, F. (deposition date: 2006-05-17, release date: 2006-11-06, Last modification date: 2023-12-13)

Primary citation

Hoffmann-Roder, A.,Schweizer, E.,Egger, J.,Seiler, P.,Obst-Sander, U.,Wagner, B.,Kansy, M.,Banner, D.W.,Diederich, F.
Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups Into the P Pocket
Chemmedchem, 1:1205-, 2006

PubMed Abstract: In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.

PubMed: 17001711
DOI: 10.1002/CMDC.200600124

Experimental method

X-RAY DIFFRACTION (1.3 Å)