3AO1

Fragment-based approach to the design of ligands targeting a novel site in HIV-1 integrase

Structural Biology Knowledgebase: 3AO1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.216

Literature

Macromolecules
Sequence Display for 3AO1

Classification: VIRAL PROTEIN / TRANSFERASE INHIBITOR

Total Structure Weight: 36564.71

Macromolecule Entities
Molecule Chains Length Organism Details
POL polyprotein A, B 163 Human immunodeficiency virus 1 Fragment: Integrase CATALYTIC CORE DOMAIN, 765-927
Mutation: C56S, W131D, F139D, F185H
Gene Name(s): pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 1,3-benzodioxol-5-ol
C7 H6 O3
LUSZGTFNYDARNI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BZX N/A in BindingDB
Kd: 5500000 nM  BindingMOAD
Kd: 5500000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.216
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.59 α = 90.00
b = 62.00 β = 90.00
c = 81.76 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-17
  • Released Date: 2011-03-09
  • Deposition author(s): Wielens, J., Parker, M.W., Chalmers, D.K., Scanlon, M.J.

Revision History

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