8VRP | pdb_00008vrp

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

PDB DOI: https://doi.org/10.2210/pdb8VRP/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-01-22 Released: 2025-07-23
Deposition Author(s): Goldstone, D.C., Walsham, L.
Funding Organization(s): Not funded

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

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of 4-Quinazolinone-bearing Phenylalanine Derivatives as HIV-1 Capsid Inhibitors with Potent and Insensitivity Towards Clinically Relevant Resistant Mutations

Zhang, X., Walsham, L., Zhan, P., Goldstone, D.C.

To be published.

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spacer peptide 1	A [auth B], B [auth C], C [auth A]	229	Human immunodeficiency virus 1	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12493
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ADQ (Subject of Investigation/LOI) Query on A1ADQ Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain F [auth C] SDF format, chain I [auth A] MOL2 format, chain D [auth B] MOL2 format, chain F [auth C] MOL2 format, chain I [auth A] mmCIF format, chain D [auth B] mmCIF format, chain F [auth C] mmCIF format, chain I [auth A]	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		Interactions Focus chain D [auth B] Focus chain F [auth C] Focus chain I [auth A] Interactions & Density Focus chain D [auth B] Focus chain F [auth C] Focus chain I [auth A]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain E [auth B] MOL2 format, chain J [auth A] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain E [auth B] mmCIF format, chain J [auth A] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain E [auth B]	E [auth B], G [auth C], H [auth C], J [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth A] Interactions & Density Focus chain E [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain J [auth A]