2VA6

X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 24

Structural Biology Knowledgebase: 2VA6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.224

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VA6

Classification: HYDROLASE

Total Structure Weight: 50899.20

Macromolecule Entities
Molecule Chains Length Organism Details
BETA SECRETASE 1 A 455 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: PROTEASE DOMAIN, RESIDUES 14-453
Mutation: R-5K, R-4K
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
H24
Query on H24

A (6S)-2-amino-6-(3'-methoxybiphenyl-3-yl)- 3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one
C19 H21 N3 O2
LQOCXPOKEPYGTJ-IBGZPJMESA-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 %)
H24 IC50: 840 nM (99) BindingDB
Ki: 270 nM (99) BindingDB

IC50: 590 nM  BindingMOAD
IC50: 670 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.224
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.97 α = 90.00
b = 102.97 β = 90.00
c = 167.28 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-08-30
  • Released Date: 2007-11-13
  • Deposition author(s): Edwards, P.D., Albert, J.S., Sylvester, M., Aharony, D., Andisik, D., Callaghan, O., Campbell, J.B., Carr, R.A., Chessari, G., Congreve, M., Frederickson, M., Folmer, R.H.A., Geschwindner, S., Koether, G., Kolmodin, K., Krumrine, J., Mauger, R.C., Murray, C.W., Olsson, L.L., Patel, S., Spear, N., Tian, G.

Revision History

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