2B8L

Crystal structure of human beta secretase complexed with inhibitor

Structural Biology Knowledgebase: 2B8L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.220

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2B8L

Classification: HYDROLASE

Total Structure Weight: 45701.94

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A 405 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: Protease domain (residues 43-446)
Mutation: K75A, E77A
Gene Name(s): BACE1 Gene View BACE KIAA1149

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
5HA
Query on 5HA

A N-[(1S,2R)-1-BENZYL-3-(CYCLOPROPYLAMINO)- 2-HYDROXYPROPYL]-5-[METHYL(METHYLSULFONYL)AMINO]- N'-[(1R)-1-PHENYLETHYL]ISOPHTHALAMIDE
C31 H38 N4 O5 S
VPNIQGRFZCTBEZ-SPTGULJVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
5HA EC50: 43 nM (99) BindingDB
IC50: 2 - 15000 nM (99) BindingDB
Ki: 233 nM (99) BindingDB

IC50: 15 nM  BindingMOAD
IC50: 15 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.220
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 104.68 α = 90.00
b = 127.92 β = 90.00
c = 76.12 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-07
  • Released Date: 2005-10-18
  • Deposition author(s): Munshi, S.K., Kuo, L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4