8VRP | pdb_00008vrp

HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.226 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.201 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8VRP

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of 4-Quinazolinone-Containing Phenylalanine Derivatives as Potent, Resistant-Tolerant HIV Capsid Inhibitors.

Zhang, X.Sun, L.Walsham, L.Ma, Y.Ding, D.Wang, M.Zhao, F.Zhang, J.Wang, Z.Xu, S.Jiang, X.Zhou, Y.De Clercq, E.Pannecouque, C.Chen, C.H.Goldstone, D.C.Liu, X.Dick, A.Zhan, P.

(2026) MedComm (2020) 7: e70746-e70746

  • DOI: https://doi.org/10.1002/mco2.70746
  • Primary Citation Related Structures: 
    8VRP

  • PubMed Abstract: 

    The HIV-1 capsid (CA) is a validated antiviral target that plays critical roles in both the early and late stages of the viral life cycle. Using structure-based strategy, we designed and synthesized a series of phenylalanine derivatives containing a 4-quinazolinone scaffold as novel HIV-1 CA inhibitors. Among them, IC-2i exhibited potent antiviral activity in MT-4 cells against HIV-1 NL4-3 (EC 50  = 0.65 ± 0.27 nM) and effectively protected cells from HIV-1 IIIB infection. SPR revealed that IC-2i interacts strongly with CA hexamers ( K D  = 2.7 ± 0.5 nM) with an extended residence time and competes with host factors CPSF6 and NUP153, disrupting CA assembly and disassembly. IC-2i retained activity against lenacapavir (LEN)-resistant strains, such as N74D (11-fold shift vs. 20-fold for LEN). Crystallographic analysis revealed that IC-2i binds at the CA NTD-CTD interface and forms hydrogen bonds with Thr107 and Ser41 (NTD-NTD interface). Pharmacological evaluation demonstrated favorable properties, including good plasma stability, low toxicity (SI > 1571), and suitable pharmacokinetics with a prolonged half-life following subcutaneous administration ( T 1/2  = 19.9 h). Overall, this study identifies 4-quinazolinone-based phenylalanine derivatives as promising HIV-1 CA inhibitors and highlights IC-2i as a potential long-acting therapeutic candidate for HIV-1 treatment.


  • Organizational Affiliation
    • Department of Medicinal Chemistry School of Pharmaceutical Sciences Key Laboratory of Chemical Biology (Ministry of Education) Shandong University Jinan Shandong China.

Macromolecule Content 

  • Total Structure Weight: 79.19 kDa 
  • Atom Count: 5,649 
  • Modeled Residue Count: 663 
  • Deposited Residue Count: 687 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spacer peptide 1A [auth B],
B [auth C],
C [auth A]
229Human immunodeficiency virus 1Mutation(s): 4 
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ADQ
(Subject of Investigation/LOI)

Query on A1ADQ



Download:Ideal Coordinates CCD File
D [auth B],
F [auth C],
I [auth A]
N-[(1S)-1-[(3P,7M)-3-{4-chloro-3-[(ethanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-7-(3-fluoro-4-formylphenyl)-4-oxo-3,4-dihydroquinazolin-2-yl]-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-yl]acetamide
C43 H32 Cl F9 N8 O5 S
AIQQZDCVPIRQSU-UHFFFAOYSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
E [auth B],
G [auth C],
H [auth C],
J [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.226 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.201 (DCC) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.268α = 90
b = 160.268β = 90
c = 57.235γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata 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: 2025-07-23
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Database references