SMTL ID : 8vrp.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

6 x 01: 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

01.1: 23 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain F: P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 15 PLIP interactions: 4 interactions with chain F, 11 interactions with chain A Hydrophobic interactions: F:Y.169, A:L.56, A:L.56, A:K.70 Hydrogen bonds: F:S.41, F:N.183, A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 Halogen bonds: F:Q.179, A:K.70 pi-Cation interactions: A:K.70, A:K.70 01.3: 23 residues within 4Å: Chain B: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain D: P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain B Hydrophobic interactions: D:Y.169, B:L.56, B:L.56, B:K.70 Hydrogen bonds: D:S.41, D:N.183, B:N.57, B:N.57, B:K.70, B:N.74, B:N.74 Halogen bonds: D:Q.179, B:K.70 pi-Cation interactions: B:K.70, B:K.70 01.5: 23 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain E: P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain E Hydrophobic interactions: C:L.56, C:L.56, C:K.70, E:Y.169 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74, E:S.41, E:N.183 pi-Cation interactions: C:K.70, C:K.70 Halogen bonds: C:K.70, E:Q.179 01.7: 23 residues within 4Å: Chain C: P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Chain D: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 15 PLIP interactions: 11 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.56, D:L.56, D:K.70, C:Y.169 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74, C:S.41, C:N.183 pi-Cation interactions: D:K.70, D:K.70 Halogen bonds: D:K.70, C:Q.179 01.9: 23 residues within 4Å: Chain A: P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Chain E: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain E Hydrophobic interactions: A:Y.169, E:L.56, E:L.56, E:K.70 Hydrogen bonds: A:S.41, A:N.183, E:N.57, E:N.57, E:K.70, E:N.74, E:N.74 Halogen bonds: A:Q.179, E:K.70 pi-Cation interactions: E:K.70, E:K.70 01.11: 23 residues within 4Å: Chain B: P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Chain F: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 15 PLIP interactions: 11 interactions with chain F, 4 interactions with chain B Hydrophobic interactions: F:L.56, F:L.56, F:K.70, B:Y.169 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74, B:S.41, B:N.183 pi-Cation interactions: F:K.70, F:K.70 Halogen bonds: F:K.70, B:Q.179

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 4 residues within 4Å: Chain A: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.8: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, X. et al., Discovery of 4-Quinazolinone-bearing Phenylalanine Derivatives as HIV-1 Capsid Inhibitors with Potent and Insensitivity Towards Clinically Relevant Resistant Mutations. To Be Published

Release Date

2025-07-23

Peptides

Spacer peptide 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Spacer peptide 1

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