6EO9

Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor

Replaces:  4NZE

Summary for 6EO9

• Entry DOI: 10.2210/pdb6eo9/pdb
• Related: 6EO8
• Descriptor: Prothrombin, Hirudin variant-2, DIMETHYL SULFOXIDE, ... (6 entities in total)
• Functional Keywords: hydrolase-hydrolase inhibitor complex, blood clotting
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 36744.46

Authors

Belviso, B.D.,Caliandro, R.,Aresta, B.M.,De Candia, M.,Altomare, C.D. (deposition date: 2017-10-09, release date: 2017-12-13, Last modification date: 2019-10-16)

Primary citation

Belviso, B.D.,Caliandro, R.,de Candia, M.,Zaetta, G.,Lopopolo, G.,Incampo, F.,Colucci, M.,Altomare, C.D.
How a beta-D-glucoside side chain enhances binding affinity to thrombin of inhibitors bearing 2-chlorothiophene as P1 moiety: crystallography, fragment deconstruction study, and evaluation of antithrombotic properties.
J. Med. Chem., 57:8563-8575, 2014

PubMed Abstract: The β-d-glucose-containing compound 3, bearing 2-chlorothiophene and 1-isopropylpiperidine moieties as binders of the S1 and S4 pockets, respectively, proved to be potent competitive inhibitor of factor Xa (fXa, Ki = 0.090 nM) and thrombin (fIIa, Ki = 100 nM). The potency of 3 increases, over the parent compound 1, against fIIa (110-fold), much more than against fXa (7-fold). Experimental deconstruction of 3 into smaller fragments revealed a binding cooperativity of the P3/P4 and propylene-linked β-d-glucose fragments, stronger in fIIa (15.5 kJ·mol(-1)) than in fXa (2.8 kJ·mol(-1)). The crystal structure of human fIIa in complex with 3 revealed a binding mode including a strong H-bond network between the glucose O1', O3', and O5' and two critical residues, namely R221a and K224, belonging to the Na(+)-binding site which may allosterically perturb the specificity sites. The potential of 3 as antithrombotic agent was supported by its ability to inhibit thrombin generation and to stimulate fibrinolysis at submicromolar concentration.

PubMed: 25268757
DOI: 10.1021/jm5010754

Experimental method

X-RAY DIFFRACTION (1.84 Å)