3AO2

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

Structural Biology Knowledgebase: 3AO2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 3AO2

Classification: VIRAL PROTEIN / TRANSFERASE INHIBITOR

Total Structure Weight: 37370.39

Macromolecule Entities
Molecule Chains Length Organism Details
POL polyprotein A, B 163 Human immunodeficiency virus 1 Fragment: Integrase CATALYTIC CORE DOMAIN, UNP residues 765-927
Mutation: C56S, S123G, T124A, K127R, W131D, F139D, F185H
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AVX
Query on AVX

A, B 3-(7-bromo-1,3-benzodioxol-5-yl)-1-methyl- 1H-pyrazol-5-amine
C11 H10 Br N3 O2
CYGCZVZRSOGLAB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTT
Query on DTT

B 2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL (Synonym)
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTV
Query on DTV

A (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-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, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
AVX N/A in BindingDB
Kd: 170000 nM  BindingMOAD
Kd: 170000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.187
  • Space Group: P 32
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.16 α = 90.00
b = 49.16 β = 90.00
c = 103.12 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-20
  • Released Date: 2011-03-16
  • Deposition author(s): Wielens, J., Chalmers, D.K., Headey, S.J., Parker, M.W., Scanlon, M.J.

Revision History

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