3RIK

The acid beta-glucosidase active site exhibits plasticity in binding 3,4,5,6-tetrahydroxyazepane-based inhibitors: implications for pharmacological chaperone design for gaucher disease

Structural Biology Knowledgebase: 3RIK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RIK

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 227128.72

Macromolecule Entities
Molecule Chains Length Organism Details
Glucosylceramidase A, B, C, D 497 Homo sapiens EC#: 3.2.1.45 IUBMB
Fragment: Residues 40-536
Mutation: R495H
Gene Name(s): GBA Gene View GC Gene View GLUC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3RI
Query on 3RI

B, D (3S,4R,5R,6S)-1-(2-hydroxyethyl)azepane-3,4,5,6- tetrol
C8 H17 N O5
VWGJHYNWDXVPIU-RULNZFCNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
3RI N/A in BindingDB
IC50: 3400000 nM  BindingMOAD
IC50: 3400000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.162
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 107.98 α = 90.00
b = 91.55 β = 110.70
c = 152.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-13
  • Released Date: 2012-03-14
  • Deposition author(s): Orwig, S.D., Lieberman, R.L.

Revision History

  • 2012-12-05
    Type: Linkage | Details: --