3NF9

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: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design

Rhodes, D.I.Peat, T.S.Vandegraaff, N.Jeevarajah, D.Le, G.Jones, E.D.Smith, J.A.Coates, J.A.Winfield, L.J.Thienthong, N.Newman, J.Lucent, D.Ryan, J.H.Savage, G.P.Francis, C.L.Deadman, J.J.

(2011) ANTIVIR.CHEM.CHEMOTHER. 21: 155-168

  • DOI: 10.3851/IMP1716
  • Primary Citation of Related Structures:  
  • Also Cited By: 3ZT4, 3ZT3, 3ZT2, 3ZT1, 3ZT0, 3ZSZ, 3ZSY, 3ZSX, 3ZSW, 3ZSV, 3ZSR, 3ZSQ

  • PubMed Abstract: 
  • HIV-1 integrase is a clinically validated therapeutic target for the treatment of HIV-1 infection, with one approved therapeutic currently on the market. This enzyme represents an attractive target for the development of new inhibitors to HIV-1 that ...

    HIV-1 integrase is a clinically validated therapeutic target for the treatment of HIV-1 infection, with one approved therapeutic currently on the market. This enzyme represents an attractive target for the development of new inhibitors to HIV-1 that are effective against the current resistance mutations.


    Organizational Affiliation

    Avexa Ltd, Richmond, Australia. drhodes@jdjbioservices.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Integrase
A, B
183Human immunodeficiency virus type 1 group M subtype B (isolate NY5)Mutation(s): 3 
Gene Names: gag-pol
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Go to UniProtKB:  P12497
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CD9
Query on CD9

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Download CCD File 
A, B
5-[(6-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-1,3-benzodioxole-4-carboxylic acid
C17 H12 Cl N O5
XVKFXTJLVSDWCE-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CD9IC50: 290000 nM BINDINGMOAD
CD9IC50: 290000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 71.379α = 90.00
b = 71.379β = 90.00
c = 66.598γ = 120.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-05-02
    Type: Database references