8TOV | pdb_00008tov

HIV-CA Disulfide linked Hexamer bound to Quinazolin-4-one Scaffold inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.260 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.223 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8TOV

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery, Crystallographic Studies, and Mechanistic Investigations of Novel Phenylalanine Derivatives Bearing a Quinazolin-4-one Scaffold as Potent HIV Capsid Modulators.

Xu, S.Sun, L.Barnett, M.Zhang, X.Ding, D.Gattu, A.Shi, D.Taka, J.R.H.Shen, W.Jiang, X.Cocklin, S.De Clercq, E.Pannecouque, C.Goldstone, D.C.Liu, X.Dick, A.Zhan, P.

(2023) J Med Chem 66: 16303-16329

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01647
  • Primary Citation Related Structures: 
    8TOV, 8TQP

  • PubMed Abstract: 

    Optimization of compound 11L led to the identification of novel HIV capsid modulators, quinazolin-4-one-bearing phenylalanine derivatives, displaying potent antiviral activities against both HIV-1 and HIV-2. Notably, derivatives 12a2 and 21a2 showed significant improvements, with 2.5-fold over 11L and 7.3-fold over PF74 for HIV-1, and approximately 40-fold over PF74 for HIV-2. The X-ray co-crystal structures confirmed the multiple pocket occupation of 12a2 and 21a2 in the binding site. Mechanistic studies revealed a dual-stage inhibition profile, where the compounds disrupted capsid-host factor interactions at the early stage and promoted capsid misassembly at the late stage. Remarkably, 12a2 and 21a2 significantly promoted capsid misassembly, outperforming 11L, PF74, and LEN. The substitution of easily metabolized amide bond with quinolin-4-one marginally enhanced the stability of 12a2 in human liver microsomes compared to controls. Overall, 12a2 and 21a2 highlight their potential as potent HIV capsid modulators, paving the way for future advancements in anti-HIV drug design.


  • Organizational Affiliation
    • Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China.

Macromolecule Content 

  • Total Structure Weight: 315.4 kDa 
  • Atom Count: 19,609 
  • Modeled Residue Count: 2,428 
  • Deposited Residue Count: 2,772 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Matrix protein p17231Human immunodeficiency virus 1Mutation(s): 4 
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12497
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J6U
(Subject of Investigation/LOI)

Query on J6U



Download:Ideal Coordinates CCD File
M [auth G]
N [auth I]
O [auth J]
P [auth K]
Q [auth L]
M [auth G],
N [auth I],
O [auth J],
P [auth K],
Q [auth L],
R [auth H],
S [auth A],
T [auth B],
U [auth C],
V [auth D],
W [auth E],
X [auth F]
2-[4-(4-aminobenzene-1-sulfonyl)-2-oxopiperazin-1-yl]-N-[(1R)-2-(3,5-difluorophenyl)-1-{3-[4-(morpholine-4-sulfonyl)phenyl]-4-oxo-3,4-dihydroquinazolin-2-yl}ethyl]acetamide
C38 H37 F2 N7 O8 S2
BUHXAJCVTIHGIR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.260 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.223 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.174α = 78.816
b = 91.326β = 87.196
c = 117.518γ = 60.116
Software Package:
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references
  • Version 1.2: 2024-11-06
    Changes: Structure summary