3VQ4

Fragments bound to HIV-1 integrase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?

Wielens, J.Headey, S.J.Rhodes, D.I.Mulder, R.J.Dolezal, O.Deadman, J.J.Newman, J.Chalmers, D.K.Parker, M.W.Peat, T.S.Scanlon, M.J.

(2013) J Biomol Screen 18: 147-159

  • DOI: https://doi.org/10.1177/1087057112465979
  • Primary Citation of Related Structures:  
    3VQ4, 3VQ5, 3VQ6, 3VQ7, 3VQ8, 3VQ9, 3VQA, 3VQB, 3VQC, 3VQD, 3VQE, 3VQP, 3VQQ, 4AH9, 4AHR, 4AHS, 4AHT, 4AHU, 4AHV

  • PubMed Abstract: 

    Fragment screening is becoming widely accepted as a technique to identify hit compounds for the development of novel lead compounds. In neighboring laboratories, we have recently, and independently, performed a fragment screening campaign on the HIV-1 integrase core domain (IN) using similar commercially purchased fragment libraries. The two campaigns used different screening methods for the preliminary identification of fragment hits; one used saturation transfer difference nuclear magnetic resonance spectroscopy (STD-NMR), and the other used surface plasmon resonance (SPR) spectroscopy. Both initial screens were followed by X-ray crystallography. Using the STD-NMR/X-ray approach, 15 IN/fragment complexes were identified, whereas the SPR/X-ray approach found 6 complexes. In this article, we compare the approaches that were taken by each group and the results obtained, and we look at what factors could potentially influence the final results. We find that despite using different approaches with little overlap of initial hits, both approaches identified binding sites on IN that provided a basis for fragment-based lead discovery and further lead development. Comparison of hits identified in the two studies highlights a key role for both the conditions under which fragment binding is measured and the criteria selected to classify hits.


  • Organizational Affiliation

    St. Vincent's Institute, Fitzroy, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POL polyprotein
A, B
158Human immunodeficiency virus 1Mutation(s): 4 
Gene Names: pol
UniProt
Find proteins for Q72498 (Human immunodeficiency virus 1)
Explore Q72498 
Go to UniProtKB:  Q72498
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72498
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0NX
Query on 0NX

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
J [auth B]
(5-phenyl-1,2-oxazol-3-yl)methanol
C10 H9 N O2
BPAFLGGUEBMWRN-UHFFFAOYSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.601α = 90
b = 62.323β = 90
c = 82.087γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
AMoREphasing
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: 2013-01-30
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description