3RIL

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: 3RIL SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RIL

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 227559.08

Macromolecule Entities
Molecule Chains Length Organism Details
Glucosylceramidase A, B, C, D 497 Homo sapiens EC#: 3.2.1.45 IUBMB
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)
3RK
Query on 3RK

A, B, C, D (3S,4R,5R,6S)-azepane-3,4,5,6-tetrol
C6 H13 N O4
MRFFNLOQLBWKPJ-UNTFVMJOSA-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 %)
3RK Ki: 12800 nM (99) BindingDB

IC50: 146000 nM  BindingMOAD
IC50: 146000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.171
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 109.22 α = 90.00
b = 91.43 β = 110.95
c = 152.66 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: --