2VA6

X-ray crystal structure of beta secretase complexed with compound 24

Summary for 2VA6

• Entry DOI: 10.2210/pdb2va6/pdb
• Related: 1FKN 1M4H 1PY1 1SGZ 1TQF 1UJJ 1UJK 1W50 1W51 1XN2 1XN3 1XS7 1YM2 1YM4 2B8L 2B8V 2VA5 2VA7
• Descriptor: BETA SECRETASE 1, IODIDE ION, (6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)-3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one, ... (4 entities in total)
• Functional Keywords: base, zymogen, protease, membrane, hydrolase, alzheimer's disease, alternative splicing, memapsin 2, glycoprotein, transmembrane, beta-secretase, aspartyl protease, aspartic protease
• Biological source: HOMO SAPIENS
• Cellular location: Membrane; Single-pass type I membrane protein: P56817
• Total number of polymer chains: 1
• Total formula weight: 50898.66

Authors

Edwards, P.D.,Albert, J.S.,Sylvester, M.,Aharony, D.,Andisik, D.,Callaghan, O.,Campbell, J.B.,Carr, R.A.,Chessari, G.,Congreve, M.,Frederickson, M.,Folmer, R.H.A.,Geschwindner, S.,Koether, G.,Kolmodin, K.,Krumrine, J.,Mauger, R.C.,Murray, C.W.,Olsson, L.L.,Patel, S.,Spear, N.,Tian, G. (deposition date: 2007-08-30, release date: 2007-11-13, Last modification date: 2023-12-13)

Primary citation

Edwards, P.D.,Albert, J.S.,Sylvester, M.,Aharony, D.,Andisik, D.,Callaghan, O.,Campbell, J.B.,Carr, R.A.,Chessari, G.,Congreve, M.,Frederickson, M.,Folmer, R.H.A.,Geschwindner, S.,Koether, G.,Kolmodin, K.,Krumrine, J.,Mauger, R.C.,Murray, C.W.,Olsson, L.L.,Patel, S.,Spear, N.,Tian, G.
Application of Fragment-Based Lead Generation to the Discovery of Novel, Cyclic Amidine Beta-Secretase Inhibitors with Nanomolar Potency, Cellular Activity, and High Ligand Efficiency.
J.Med.Chem., 50:5912-, 2007

PubMed Abstract: Fragment-based lead generation has led to the discovery of a novel series of cyclic amidine-based inhibitors of beta-secretase (BACE-1). Initial fragment hits with an isocytosine core having millimolar potency were identified via NMR affinity screening. Structure-guided evolution of these fragments using X-ray crystallography together with potency determination using surface plasmon resonance and functional enzyme inhibition assays afforded micromolar inhibitors. Similarity searching around the isocytosine core led to the identification of a related series of inhibitors, the dihydroisocytosines. By leveraging the knowledge of the ligand-BACE-1 recognition features generated from the isocytosines, the dihydroisocytosines were efficiently optimized to submicromolar potency. Compound 29, with an IC50 of 80 nM, a ligand efficiency of 0.37, and cellular activity of 470 nM, emerged as the lead structure for future optimization.

PubMed: 17985862
DOI: 10.1021/JM070829P

Experimental method

X-RAY DIFFRACTION (2.5 Å)