6DMI

A multiconformer ligand model of 5T5 bound to BACE-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5EZX - determined by Banner, D., Benz, J., Stihle, M., Kuglstatter, A.  

Literature

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps.

van Zundert, G.Hudson, B.M.de Oliveira, S.Keedy, D.A.Fonseca, R.Heliou, A.Suresh, P.Borrelli, K.Day, T.Fraser, J.van den Bedem, H.

(2018) J. Med. Chem. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 1
A
390Homo sapiensMutation(s): 0 
Gene Names: BACE1 (BACE, KIAA1149)
EC: 3.4.23.46
Find proteins for P56817 (Homo sapiens)
Go to Gene View: BACE1
Go to UniProtKB:  P56817
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5T5
Query on 5T5

Download SDF File 
Download CCD File 
A
[(1~{R},2~{R})-2-[(4~{S})-2-azanyl-4-[4-[bis(fluoranyl)methoxy]phenyl]-5~{H}-1,3-oxazol-4-yl]cyclopropyl]-(5-chloranylpyridin-3-yl)methanone
C19 H16 Cl F2 N3 O3
AVRZQFKBYKMVDH-SPYBWZPUSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.320α = 90.00
b = 102.320β = 90.00
c = 169.820γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release