2FDP

Crystal structure of beta-secretase complexed with an amino-ethylene inhibitor

Structural Biology Knowledgebase: 2FDP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.225

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FDP

Classification: HYDROLASE

Total Structure Weight: 131450.72

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A, B, C 388 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
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
FRP
Query on FRP

A, B, C N1-((2S,3S,5R)-3-AMINO-6-(4-FLUOROPHENYLAMINO)- 5-METHYL-6-OXO-1-PHENYLHEXAN-2-YL)-N3,N3- DIPROPYLISOPHTHALAMIDE
C33 H41 F N4 O3
PZHFCAIXAVDQAK-STQWGSIPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FRP Ki: 26 nM (100) BindingDB

Ki: 26 nM  BindingMOAD
Ki: 26 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.225
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.19 α = 90.00
b = 102.19 β = 103.21
c = 99.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-14
  • Released Date: 2006-01-24
  • Deposition author(s): Yang, W., Lu, W., Lu, Y., Zhong, M., Sun, J., Thomas, A.E., Wilkinson, J.M., Fucini, R.V., Lam, M., Randal, M., Shi, X.P., Jacobs, J.W., McDowell, R.S., Gordon, E.M., Ballinger, M.D.

Revision History

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