ISDA: 5QD7

Deposition Date 2017-12-01

Release Date 2020-06-03

Last Version Date 2024-10-23

Entry Detail

PDB ID:

5QD7

Keywords:

HYDROLASE

Title:

Crystal structure of BACE complex with BMC014

Biological Source:

Source Organism(s):

Homo sapiens (Taxon ID: 9606)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.12 Å

R-Value Free:

0.18

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Beta-secretase 1
Gene (Uniprot):BACE1
Chain IDs:A, B, C
Chain Length:402
Number of Molecules:3
Biological Source:Homo sapiens

UniProt ID:P56817 Pfam ID:PF00026 EC:3.4.23.46

Ligand Molecules

0BI

Primary Citation

D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.

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, Lerchner, A, Machauer, R, Betschart, C, Veenstra, S, Rueeger, H, McCarthy, C, Tintelnot-Blomley, M, Jaton, A.L, Rabe, S, Desrayaud, S, Enz, A, Staufenbiel, M, Paganetti, P, Rondeau, J.M, Neumann, U.Show

J.Comput.Aided Mol.Des. 34 99 119 (2020)

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

Abstact

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.

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Primary Citation of related structures

Abstact

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