3S2O

Fragment based discovery and optimisation of bace-1 inhibitors

Structural Biology Knowledgebase: 3S2O SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3S2O

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 46090.19

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A 408 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: UNP RESIDUES 46-453
Gene Name(s): BACE1 Gene View BACE KIAA1149
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EV6
Query on EV6

A (3S)-3-(2-amino-5-chloro-1H-benzimidazol- 1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec- 2-yl]pentanamide
C22 H29 Cl N4 O
KMAKOMVKNWTGPE-LIXZBVSLSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
EV6 IC50: 8900 nM (100) BindingDB

N/A in BindingMoad
IC50: 8900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.205
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 101.88 α = 90.00
b = 101.88 β = 90.00
c = 170.18 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-17
  • Released Date: 2011-06-01
  • Deposition author(s): Madden, J., Godemann, R., Smith, M.A., Hallett, D., Barker, J., Kraemer, J.
  • Previous versions: 3MSM

Revision History

  • 2011-09-07
    Type: Function and keywords | Details: --
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4