3ENS

Crystal structure of human FXA in complex with methyl (2Z)-3-[(3-chloro-1H-indol-7-yl)amino]-2-cyano-3-{[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]amino}acrylate

Summary for 3ENS

• Entry DOI: 10.2210/pdb3ens/pdb
• Descriptor: Factor X light chain, Activated factor Xa heavy chain, GLYCEROL, ... (9 entities in total)
• Functional Keywords: serine protease, hydrolase, epidermal growth factor like domain, blood coagulation factor, cleavage on pair of basic residues, egf-like domain, gamma-carboxyglutamic acid, glycoprotein, hydroxylation, zymogen, blood clotting
• Biological source: Homo sapiens (Human); More
• Cellular location: Secreted: P00742 P00742
• Total number of polymer chains: 4
• Total formula weight: 76475.27

Authors

Klei, H.E. (deposition date: 2008-09-25, release date: 2008-12-30, Last modification date: 2017-10-25)

Primary citation

Shi, Y.,Sitkoff, D.,Zhang, J.,Klei, H.E.,Kish, K.,Liu, E.C.,Hartl, K.S.,Seiler, S.M.,Chang, M.,Huang, C.,Youssef, S.,Steinbacher, T.E.,Schumacher, W.A.,Grazier, N.,Pudzianowski, A.,Apedo, A.,Discenza, L.,Yanchunas, J.,Stein, P.D.,Atwal, K.S.
Design, Structure-Activity Relationships, X-ray Crystal Structure, and Energetic Contributions of a Critical P1 Pharmacophore: 3-Chloroindole-7-yl-Based Factor Xa Inhibitors.
J.Med.Chem., 51:7541-7551, 2008

PubMed Abstract: An indole-based P1 moiety was incorporated into a previously established factor Xa inhibitor series. The indole group was designed to hydrogen-bond with the carbonyl of Gly218, while its 3-methyl or 3-chloro substituent was intended to interact with Tyr228. These interactions were subsequently observed in the X-ray crystal structure of compound 18. SAR studies led to the identification of compound 20 as the most potent FXa inhibitor in this series (IC(50) = 2.4 nM, EC(2xPT) = 1.2 microM). An in-depth energetic analysis suggests that the increased binding energy of 3-chloroindole-versus 3-methylindole-containing compounds in this series is due primarily to (a) the more hydrophobic nature of chloro- versus methyl-containing compounds and (b) an increased interaction of 3-chloroindole versus 3-methylindole with Gly218 backbone. The stronger hydrophobicity of chloro- versus methyl-substituted aromatics may partly explain the general preference for chloro- versus methyl-substituted P1 groups in FXa, which extends beyond the current series.

PubMed: 18998662
DOI: 10.1021/jm800855x

Experimental method

X-RAY DIFFRACTION (2.3 Å)