3AO5

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

Structural Biology Knowledgebase: 3AO5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.243

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3AO5

Classification: VIRAL PROTEIN / TRANSFERASE INHIBITOR

Total Structure Weight: 37572.01

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): pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SUC
Query on SUC

A SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BBY
Query on BBY

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

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

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BBY N/A in BindingDB
Kd: 5900000 nM  BindingMOAD
Kd: 5900000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.243
  • Space Group: P 32
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 49.03 α = 90.00
b = 49.03 β = 90.00
c = 103.72 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-21
  • Released Date: 2011-03-09
  • Deposition author(s): Wielens, J., Headey, S.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