4DUS

Structure of Bace-1 (Beta-Secretase) in complex with N-((2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-((6'-neopentyl-3',4'-dihydrospiro[cyclobutane-1,2'-pyrano[2,3-b]pyridin]-4'-yl)amino)butan-2-yl)acetamide

Structural Biology Knowledgebase: 4DUS SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DUS

Classification: HYDROLASE / Hydrolase Inhibitor

Total Structure Weight: 47379.07

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A 411 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: UNP residues 43-453
Mutation: R-5K, R-4K
Gene Name(s): BACE1 Gene View BACE KIAA1149

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
0MP
Query on 0MP

A N-((2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4- ((6'-neopentyl-3',4'-dihydrospiro[cyclobutane- 1,2'-pyrano[2,3-b]pyridin]-4'-yl)amino)butan- 2-yl)acetamide
C28 H38 F N3 O3
FBJQDUYQPYABBR-CCDWMCETSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0MP IC50: 5 - 13 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.221
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.31 α = 90.00
b = 102.31 β = 90.00
c = 169.76 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-22
  • Released Date: 2012-10-10
  • Deposition author(s): Sickmier, E.A.

Revision History

  • 2014-07-02
    Type: Citation | Details: Citation update