2VA5

X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 8C

Structural Biology Knowledgebase: 2VA5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.319
  • R-Value Work: 0.228

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VA5

Classification: HYDROLASE

Total Structure Weight: 50703.20

Macromolecule Entities
Molecule Chains Length Organism Details
BETA-SECRETASE 1 . A 455 Homo sapiens EC#: 3.4.23.46 IUBMB
Fragment: PROTEASE DOMAIN, RESIDUES 14-453
Mutation: R-5K, R-4K
Gene Name(s): BACE1 Gene View BACE KIAA1149

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C8C
Query on C8C

A 2-amino-6-[2-(1H-indol-6-yl)ethyl]pyrimidin- 4(3H)-one
C14 H14 N4 O
VRAZIAJSKFRSIP-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
IOD
Query on IOD

A IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
C8C IC50: 86000 - 130000 nM (99) BindingDB

N/A in BindingMoad
IC50: 86000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.319
  • R-Value Work: 0.228
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.14 α = 90.00
b = 102.14 β = 90.00
c = 168.26 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., Patel, S., Spear, N., Tian, G.

Revision History

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