8QUL

Hexameric HIV-1 CA in complex with DDD00100555


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments.

Lang, S.Fletcher, D.A.Petit, A.P.Luise, N.Fyfe, P.Zuccotto, F.Porter, D.Hope, A.Bellany, F.Kerr, C.Mackenzie, C.J.Wyatt, P.G.Gray, D.W.

(2024) ChemMedChem 19: e202400025-e202400025

  • DOI: https://doi.org/10.1002/cmdc.202400025
  • Primary Citation of Related Structures:  
    8QUB, 8QUH, 8QUI, 8QUJ, 8QUK, 8QUL, 8QUW, 8QUX, 8QUY, 8QV1, 8QV4, 8QV9, 8QVA

  • PubMed Abstract: 

    Identification and assessment of novel targets is essential to combat drug resistance in the treatment of HIV/AIDS. HIV Capsid (HIV-CA), the protein playing a major role in both the early and late stages of the viral life cycle, has emerged as an important target. We have applied an NMR fragment screening platform and identified molecules that bind to the N-terminal domain (NTD) of HIV-CA at a site close to the interface with the C-terminal domain (CTD). Using X-ray crystallography, we have been able to obtain crystal structures to identify the binding mode of these compounds. This allowed for rapid progression of the initial, weak binding, fragment starting points to compounds 37 and 38, which have 19F-pKi values of 5.3 and 5.4 respectively.


  • Organizational Affiliation

    University of Dundee School of Life Sciences, Drug Discovery Unit, UNITED KINGDOM.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spacer peptide 1231Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12493 
Go to UniProtKB:  P12493
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12493
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3IP (Subject of Investigation/LOI)
Query on 3IP

Download Ideal Coordinates CCD File 
B [auth A]3-(BENZYLOXY)PYRIDIN-2-AMINE
C12 H12 N2 O
NMCBWICNRJLKKM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.65α = 90
b = 90.65β = 90
c = 56.68γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-27
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references
  • Version 1.2: 2024-07-10
    Changes: Database references
  • Version 1.3: 2024-10-16
    Changes: Structure summary