3UDK

Crystal Structure of BACE with Compound 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 3UDK

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 45834.16

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A 404 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: UNP residues 58-453
Gene Name(s): BACE1 Gene View BACE KIAA1149
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
095
Query on 095

A tetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2- dihydrospiro[indole-3,3'-pyrrolidine]-5'- carboxylate
C17 H20 N2 O4
HIOAPSYSJQPIRC-RHSMWYFYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
095 IC50: 32000 - 114000 nM (100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.306
  • R-Value Work: 0.219
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 74.80 α = 90.00
b = 104.43 β = 90.00
c = 101.33 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-10-28
  • Released Date: 2012-04-18
  • Deposition author(s): Efremov, I.V., Vajdos, F.F., Borzilleri, K., Capetta, S., Dorff, P., Dutra, J., Mansour, M., Oborski, C., O'Connell, T., O'Sullivan, T.J., Pandit, J., Wang, H., Withka, J.

Revision History

  • 2013-06-19
    Type: Database references