2ZJM

Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(5-chloro-2-isopropoxy-3-methoxy-benzyl)-piperidin-4-yl]-2-(4-sulfamoyl-phenoxy)-acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Fragment-based discovery of novel BACE1 inhibitors using Tethering technology

Yang, W.Fucini, R.V.Fahr, B.T.Randal, M.Lind, K.E.Lam, M.B.Lu, W.Lu, Y.Cary, D.R.Romanowski, M.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-secretase 1405Homo sapiensMutation(s): 2 
Gene Names: BACE1
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
GTEx:  ENSG00000186318 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56817
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F1M
Query on F1M

Download Ideal Coordinates CCD File 
B [auth A]N-{1-[5-chloro-3-methoxy-2-(1-methylethoxy)benzyl]piperidin-4-yl}-2-(4-sulfamoylphenoxy)acetamide
C24 H32 Cl N3 O6 S
QVZLZLJHCAPQQC-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.645α = 90
b = 127.836β = 90
c = 76.561γ = 90
Software Package:
Software NamePurpose
CNXrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary