3VQP

HIV-1 IN core domain in complex with 2,3-dihydro-1,4-benzodioxin-5-ylmethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1177/1087057112465979
  • Primary Citation of Related Structures:  3VQ4, 3VQ5, 3VQ6, 3VQ7, 3VQ8, 3VQ9, 3VQA, 3VQB, 3VQC, 3VQD, 3VQE, 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- ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POL polyprotein
A, B
158Human immunodeficiency virus 1Gene Names: pol
Find proteins for Q72498 (Human immunodeficiency virus 1)
Go to UniProtKB:  Q72498
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DBJ
Query on DBJ

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Download CCD File 
A
2,3-dihydro-1,4-benzodioxin-5-ylmethanol
C9 H10 O3
WATIARBIFSKYKC-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.850α = 90.00
b = 63.180β = 90.00
c = 82.130γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
AMoREphasing
XSCALEdata scaling
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-30
    Type: Initial release