2VA7

X-RAY CRYSTAL STRUCTURE OF BETA SECRETASE COMPLEXED WITH COMPOUND 27

Structural Biology Knowledgebase: 2VA7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.223

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VA7

Classification: HYDROLASE

Total Structure Weight: 50927.26

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

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C27
Query on C27

A (6R)-2-amino-6-[2-(3'-methoxybiphenyl-3-yl)ethyl]- 3,6-dimethyl-5,6-dihydropyrimidin-4(3H)-one
C21 H25 N3 O2
VDFBMQAUECXNKR-OAQYLSRUSA-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 %)
C27 IC50: 80 - 470 nM (99) BindingDB

IC50: 640 nM  BindingMOAD
IC50: 200 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.223
  • Space Group: P 61 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 102.69 α = 90.00
b = 102.69 β = 90.00
c = 168.34 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