5QDB

Crystal structure of BACE complex with BMC002

Summary for 5QDB

• Entry DOI: 10.2210/pdb5qdb/pdb
• Group deposition: Crystal Structures of Beta-Secretase 1 with Bound Ligands (G_1002044)
• Descriptor: Beta-secretase 1, (3S,14R,16S)-16-[(1R)-1-hydroxy-2-{[3-(1-methylethyl)benzyl]amino}ethyl]-3,4,14-trimethyl-1,4-diazacyclohexadecane-2,5- dione (3 entities in total)
• Functional Keywords: hydroloase, d3r, bace, ligand docking, hydrolase
• Biological source: homo sapiens
• Total number of polymer chains: 3
• Total formula weight: 135795.16

Authors

Rondeau, J.M.,Shao, C.,Yang, H.,Burley, S.K. (deposition date: 2017-12-01, release date: 2020-06-03, Last modification date: 2021-02-10)

Primary citation

Parks, C.D.,Gaieb, Z.,Chiu, M.,Yang, H.,Shao, C.,Walters, W.P.,Jansen, J.M.,McGaughey, G.,Lewis, R.A.,Bembenek, S.D.,Ameriks, M.K.,Mirzadegan, T.,Burley, S.K.,Amaro, R.E.,Gilson, M.K.
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
J.Comput.Aided Mol.Des., 34:99-119, 2020

PubMed Abstract: The Drug Design Data Resource (D3R) aims to identify best practice methods for computer aided drug design through blinded ligand pose prediction and affinity challenges. Herein, we report on the results of Grand Challenge 4 (GC4). GC4 focused on proteins beta secretase 1 and Cathepsin S, and was run in an analogous manner to prior challenges. In Stage 1, participant ability to predict the pose and affinity of BACE1 ligands were assessed. Following the completion of Stage 1, all BACE1 co-crystal structures were released, and Stage 2 tested affinity rankings with co-crystal structures. We provide an analysis of the results and discuss insights into determined best practice methods.

PubMed: 31974851
DOI: 10.1007/s10822-020-00289-y

Experimental method

X-RAY DIFFRACTION (2.1 Å)