3NF7

Structural basis for a new mechanism of inhibition of HIV integrase identified by fragment screening and structure based design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 3NF7

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 42285.94

Macromolecule Entities
Molecule Chains Length Organism Details
Integrase A, B 183 Human immunodeficiency virus 1 Fragment: catalytic domain, UNP residues 50-212
Mutation: C56S, F139D, F185H
Gene Name(s): gag-pol
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CIW
Query on CIW

A, B 5-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1- yl)methyl]-1,3-benzodioxole-4-carboxylic acid
C17 H12 Cl N O5
ZWUIUQQUOGIKGU-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)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACY
Query on ACY

A, B ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CIW N/A in BindingDB
IC50: 340000 nM  BindingMOAD
IC50: 340000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.162
  • Space Group: P 31

Unit Cell:

Length (Å) Angle (°)
a = 71.33 α = 90.00
b = 71.33 β = 90.00
c = 66.92 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-06-09
  • Released Date: 2011-04-27
  • Deposition author(s): Peat, T.S., Newman, J., Deadman, J.J., Rhodes, D.

Revision History

  • 2011-07-13
    Type: Version format compliance
  • 2012-05-02
    Type: Database references