5QCU

Crystal structure of BACE complex with BMC022


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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.

(2020) J Comput Aided Mol Des 34: 99-119

  • DOI: 10.1007/s10822-020-00289-y
  • Primary Citation of Related Structures:  
    5QDA, 5QDC, 5QDB, 5QDD, 5QCX, 5QD9, 5QCW, 5QD8, 5QCZ, 5QCY, 5QCP, 5QD1, 5QCO, 5QD0, 5QCR, 5QD3, 5QCQ, 5QD2, 5QCT, 5QD5, 5QCS, 5QD4, 5QCV, 5QD7, 5QCU, 5QD6

  • 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 ...

    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.


    Organizational Affiliation

    Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, 9500 Gilman Drive, MC0751, La Jolla, CA, 92093, USA. mgilson@ucsd.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-secretase 1A, B, C402Homo sapiensMutation(s): 0 
Gene Names: BACE1BACEKIAA1149
EC: 3.4.23.46
UniProt & NIH Common Fund Data Resources
Find proteins for P56817 (Homo sapiens)
Explore P56817 
Go to UniProtKB:  P56817
PHAROS:  P56817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E51 (Subject of Investigation/LOI)
Query on E51

Download Ideal Coordinates CCD File 
D [auth A], E [auth B], F [auth C](2R,4S)-N-butyl-4-[(5S,8S,10R)-5,10-dimethyl-3,3,6-trioxo-3lambda~6~-thia-7-azabicyclo[11.3.1]heptadeca-1(17),13,15-trien-8-yl]-4-hydroxy-2-methylbutanamide
C26 H42 N2 O5 S
RYVHNXNTYFQKLT-FSQPGOEKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.173α = 90
b = 102.482β = 103.67
c = 100.443γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNXrefinement
CNXphasing
SCALEPACKdata scaling
DENZOdate reduction
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-12-30
    Changes: Structure summary
  • Version 1.2: 2021-02-10
    Changes: Database references