2VKM

CRYSTAL STRUCTURE OF GRL-8234 BOUND TO BACE (BETA-SECRETASE)

Structural Biology Knowledgebase: 2VKM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 2VKM

Classification: HYDROLASE

Total Structure Weight: 175888.23

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-SECRETASE 1 A, B, C, D 389 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: BETA-SECRETASE CATALYTIC DOMAIN, RESIDUES 58-446
Details: BETA SECRETASE INHIBITOR
Gene Name(s): BACE1 Gene View BACE KIAA1149
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D N-{(1S,2R)-1-benzyl-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}- 5-[methyl(methylsulfonyl)amino]-N'-[(1R)- 1-phenylethyl]benzene-1,3-dicarboxamide
C36 H42 N4 O6 S
HIQWWDCRULXYDF-SWROZOJRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BSD IC50: 1 - 2.5 nM (100) BindingDB
Ki: 1.8 nM (100) BindingDB

Ki: 1.8 nM  BindingMOAD
Ki: 1.8 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.202
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.70 α = 90.00
b = 130.31 β = 97.41
c = 87.71 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-04
  • Released Date: 2008-12-16
  • Deposition author(s): Hong, L., Tang, J., Ghosh, A.K.

Revision History

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