3NF8

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: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

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Ligand Structure Quality Assessment 


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:  
    3NF6, 3NF7, 3NF8, 3NF9, 3NFA

  • 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 are effective against the current resistance mutations ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseA, B183Human immunodeficiency virus 1Mutation(s): 3 
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDQ (Subject of Investigation/LOI)
Query on CDQ

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A], N [auth B], O [auth B]6-[(5-chloro-2-oxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
C18 H14 Cl N O5
KBLBOZBAVQRJSU-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACY
Query on ACY

Download Ideal Coordinates CCD File 
J [auth A], P [auth B]ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
CDQ PDBBind:  3NF8 IC50: 1.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.549α = 90
b = 71.549β = 90
c = 67.099γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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