8FIU: HIV-1 capsid

Potent long-acting inhibitors targeting HIV-1 capsid based on a versatile quinazolin-4-one scaffold. Determined by X-ray diffraction at 1.56 Å resolution. Released 15 Feb 2023.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Human immunodeficiency virus 1
Chains: 3
Atoms: 6,150
Mol. weight: 79.97 kDa
Ligands: Y05
Released: 15 Feb 2023

Explore 8FIU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FIU contains 48 α-helices and 6 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	10-12	3	1
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	85-88	4
α-helix	96-99	4
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-189	11
α-helix	196-205	10
α-helix	211-217	7

Chain B: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	10-12	3	2
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	85-88	4
α-helix	90-92	3
α-helix	95-99	5
α-helix	101-104	4
α-helix	111-119	9
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-175	15
α-helix	185-188	4
α-helix	189-192	4
α-helix	196-205	10
α-helix	211-217	7

Chain C: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	3
β-strand	9-12	4	3
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	85-88	4
α-helix	90-92	3
α-helix	95-99	5
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-192	14
α-helix	196-205	10
α-helix	211-218	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 capsid	A, B, C	protein	232	Human immunodeficiency virus 1	P12493

Sequence of entity 1 (A, B, C), FASTA

>8FIU_1 HIV-1 capsid (chains A, B, C)
MPIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTV
GGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMT
HNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQ
EVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Ligands and cofactors

ID	Name	Formula	Copies
Y05	N-[(1S)-1-{(3P)-3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl…	C41 H38 Cl F6 N9 O5 S	3

Water and common crystallization additives (EDO) are not listed.

Primary citation

Potent Long-Acting Inhibitors Targeting the HIV-1 Capsid Based on a Versatile Quinazolin-4-one Scaffold. Gillis, E.P., Parcella, K., Bowsher, M. et al. J Med Chem (2023) 66:1941-1954. DOI 10.1021/acs.jmedchem.2c01732 · PubMed

Other PDB entries of the same protein (UniProt P12493), best resolution first:

8QUK 1.38 Å, Hexameric HIV-1 CA in complex with DDD00100439
8QUH 1.55 Å, Hexameric HIV-1 CA in complex with DDD00057456
8QUB 1.63 Å, Hexameric HIV-1 CA in complex with DDD00074110
8QUJ 1.63 Å, Hexameric HIV-1 CA in complex with DDD00100452
8QUL 1.67 Å, Hexameric HIV-1 CA in complex with DDD00100555
8QUI 1.69 Å, Hexameric HIV-1 CA in complex with DDD00024969
5JPA 1.7 Å, Hexameric HIV-1 CA H12Y mutant
8QV9 1.76 Å, Hexameric HIV-1 CA in complex with DDD01829021
4U0C 1.77 Å, Hexameric HIV-1 CA in complex with Nup153 peptide, P6 crystal form
8VRP 1.8 Å, HIV-CA Disulfide linked Hexamer bound to 4-Quinazolinone Scaffold inhibitor
8QUY 1.88 Å, Hexameric HIV-1 CA in complex with DDD01728501
5TSX 1.9 Å, HIV-1 CA hexamer with NUP153 peptide - P1 crystal form

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