4GID

Structure of beta-secretase complexed with inhibitor

Structural Biology Knowledgebase: 4GID SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GID

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 176144.75

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-secretase 1 A, B, C, D 388 Homo sapiens EC#: 3.4.23.46 IUBMB 4.3.1.23 IUBMB
Fragment: CATALYTIC DOMAIN
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
0GH
Query on 0GH

A, B, C, D N-[(2S)-1-({(2S,3R)-3-hydroxy-1-[(2-methylpropyl)amino]- 1-oxobutan-2-yl}amino)-3-phenylpropan-2-yl]- 5-[methyl(methylsulfonyl)amino]-N'-[(1R)- 1-phenylethyl]benzene-1,3-dicarboxamide
C35 H47 N5 O6 S
UZFAOTIMARRSKT-TYUOOWEOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LPD
Query on LPD

A, B, C, D L-PROLINAMIDE
C5 H10 N2 O
VLJNHYLEOZPXFW-BYPYZUCNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
0GH IC50: >1000 nM (100) BindingDB
Ki: 99 nM (100) BindingDB

Ki: 0.017 nM  BindingMOAD
Ki: 0.017 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.216
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 86.43 α = 90.00
b = 130.35 β = 97.50
c = 88.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-08
  • Released Date: 2012-10-10
  • Deposition author(s): Ghosh, A., Tang, J., Venkateswara, R.K., Yadav, N., Anderson, D., Gavande, N., Huang, X., Terzyan, S.

Revision History

  • 2013-08-28
    Type: Citation | Details: Citation update