5LRK

Crystal structure of the porcine carboxypeptidase B - Anabaenopeptin F complex

Summary for 5LRK

• Entry DOI: 10.2210/pdb5lrk/pdb
• Descriptor: Carboxypeptidase B, Anabaenopeptin F, ZINC ION, ... (4 entities in total)
• Functional Keywords: drug discovery, natural compound, tafi inhibitor, anabaenopeptin, hydrolase
• Biological source: Sus scrofa (Pig); More
• Cellular location: Secreted : P09955
• Total number of polymer chains: 6
• Total formula weight: 107022.86

Authors

Schreuder, H.,Liesum, A.,Loenze, P. (deposition date: 2016-08-19, release date: 2016-09-21, Last modification date: 2024-11-13)

Primary citation

Schreuder, H.,Liesum, A.,Lonze, P.,Stump, H.,Hoffmann, H.,Schiell, M.,Kurz, M.,Toti, L.,Bauer, A.,Kallus, C.,Klemke-Jahn, C.,Czech, J.,Kramer, D.,Enke, H.,Niedermeyer, T.H.,Morrison, V.,Kumar, V.,Bronstrup, M.
Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).
Sci Rep, 6:32958-32958, 2016

PubMed Abstract: Mature thrombin activatable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help to prevent thrombosis. Applying a lead finding approach based on literature-mining, we discovered that anabaenopeptins, cyclic peptides produced by cyanobacteria, were potent inhibitors of TAFIa with IC50 values as low as 1.5 nM. We describe the isolation and structure elucidation of 20 anabaenopeptins, including 13 novel congeners, as well as their pronounced structure-activity relationships (SAR) with respect to inhibition of TAFIa. Crystal structures of the anabaenopeptins B, C and F bound to the surrogate protease carboxypeptidase B revealed the binding modes of these large (~850 Da) compounds in detail and explained the observed SAR, i.e. the strong dependence of the potency on a basic (Arg, Lys) exocyclic residue that addressed the S1' binding pocket, and a broad tolerance towards substitutions in the pentacyclic ring that acted as a plug of the active site.

PubMed: 27604544
DOI: 10.1038/srep32958

Experimental method

X-RAY DIFFRACTION (2.3 Å)