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

Potent long-acting inhibitors targeting HIV-1 capsid based on a versatile quinazolin-4-one scaffold

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-hexamer

Ligands

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: S.34, P.35, E.36, K.171, R.174 Chain F: V.60, G.61, G.62, Q.64 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Water bridges: A:S.34, A:S.34 Hydrogen bonds: F:V.60, F:G.62 EDO.2: 7 residues within 4Å: Chain A: E.77, E.80, W.81, L.84, I.130, R.133, W.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.77, A:R.133, A:W.134 EDO.4: 9 residues within 4Å: Chain B: S.34, P.35, E.36, K.171, R.174 Chain D: V.60, G.61, G.62, Q.64 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:V.60, D:G.62 Water bridges: B:S.34, B:S.34 EDO.5: 7 residues within 4Å: Chain B: E.77, E.80, W.81, L.84, I.130, R.133, W.134 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.77, B:R.133, B:W.134 EDO.7: 9 residues within 4Å: Chain C: S.34, P.35, E.36, K.171, R.174 Chain E: V.60, G.61, G.62, Q.64 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain E Water bridges: C:S.34, C:S.34 Hydrogen bonds: E:V.60, E:G.62 EDO.8: 7 residues within 4Å: Chain C: E.77, E.80, W.81, L.84, I.130, R.133, W.134 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.77, C:R.133, C:W.134 EDO.10: 9 residues within 4Å: Chain C: V.60, G.61, G.62, Q.64 Chain D: S.34, P.35, E.36, K.171, R.174 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:S.34, D:S.34 Hydrogen bonds: C:V.60, C:G.62 EDO.11: 7 residues within 4Å: Chain D: E.77, E.80, W.81, L.84, I.130, R.133, W.134 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.77, D:R.133, D:W.134 EDO.13: 9 residues within 4Å: Chain A: V.60, G.61, G.62, Q.64 Chain E: S.34, P.35, E.36, K.171, R.174 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:V.60, A:G.62 Water bridges: E:S.34, E:S.34 EDO.14: 7 residues within 4Å: Chain E: E.77, E.80, W.81, L.84, I.130, R.133, W.134 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.77, E:R.133, E:W.134 EDO.16: 9 residues within 4Å: Chain B: V.60, G.61, G.62, Q.64 Chain F: S.34, P.35, E.36, K.171, R.174 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain B Water bridges: F:S.34, F:S.34 Hydrogen bonds: B:V.60, B:G.62 EDO.17: 7 residues within 4Å: Chain F: E.77, E.80, W.81, L.84, I.130, R.133, W.134 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.77, F:R.133, F:W.134

6 x Y05: N-[(1S)-1-{(3P)-3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-7-[(2R,6S)-2,6-dimethylmorpholin-4-yl]-4-oxo-3,4-dihydroquinazolin-2-yl}-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-3-(difluoromethyl)-5,5-difluoro-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide(Non-covalent)

Y05.3: 24 residues within 4Å: Chain A: N.54, L.57, N.58, Q.64, M.67, Q.68, L.70, K.71, I.74, N.75, A.106, G.107, T.108, Y.131 Chain E: I.38, P.39, S.42, I.136, Y.170, L.173, R.174, Q.180, K.183, N.184 23 PLIP interactions: 17 interactions with chain A, 6 interactions with chain E Hydrophobic interactions: A:L.57, A:L.57, A:K.71, E:I.38, E:Y.170, E:Y.170 Hydrogen bonds: A:N.54, A:N.58, A:N.58, A:K.71, A:N.75, A:T.108, E:N.184 Water bridges: A:Q.68, A:Q.68, A:N.75 pi-Cation interactions: A:K.71, A:K.71, A:K.71 Halogen bonds: A:K.71, A:N.75, E:Y.170, E:R.174 Y05.6: 24 residues within 4Å: Chain B: N.54, L.57, N.58, Q.64, M.67, Q.68, L.70, K.71, I.74, N.75, A.106, G.107, T.108, Y.131 Chain F: I.38, P.39, S.42, I.136, Y.170, L.173, R.174, Q.180, K.183, N.184 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain F Hydrophobic interactions: B:L.57, B:L.57, B:K.71, F:I.38, F:Y.170, F:Y.170 Hydrogen bonds: B:N.54, B:N.58, B:N.58, B:K.71, B:N.75, B:T.108, F:N.184 Water bridges: B:Q.68, B:Q.68, B:N.75 pi-Cation interactions: B:K.71, B:K.71, B:K.71 Halogen bonds: B:K.71, B:N.75, F:Y.170, F:R.174 Y05.9: 24 residues within 4Å: Chain C: N.54, L.57, N.58, Q.64, M.67, Q.68, L.70, K.71, I.74, N.75, A.106, G.107, T.108, Y.131 Chain D: I.38, P.39, S.42, I.136, Y.170, L.173, R.174, Q.180, K.183, N.184 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain D Hydrophobic interactions: C:L.57, C:L.57, C:K.71, D:I.38, D:Y.170, D:Y.170 Hydrogen bonds: C:N.54, C:N.58, C:N.58, C:K.71, C:N.75, C:T.108, D:N.184 Water bridges: C:Q.68, C:Q.68, C:N.75 pi-Cation interactions: C:K.71, C:K.71, C:K.71 Halogen bonds: C:K.71, C:N.75, D:Y.170, D:R.174 Y05.12: 24 residues within 4Å: Chain B: I.38, P.39, S.42, I.136, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain D: N.54, L.57, N.58, Q.64, M.67, Q.68, L.70, K.71, I.74, N.75, A.106, G.107, T.108, Y.131 23 PLIP interactions: 17 interactions with chain D, 6 interactions with chain B Hydrophobic interactions: D:L.57, D:L.57, D:K.71, B:I.38, B:Y.170, B:Y.170 Hydrogen bonds: D:N.54, D:N.58, D:N.58, D:K.71, D:N.75, D:T.108, B:N.184 Water bridges: D:Q.68, D:Q.68, D:N.75 pi-Cation interactions: D:K.71, D:K.71, D:K.71 Halogen bonds: D:K.71, D:N.75, B:Y.170, B:R.174 Y05.15: 24 residues within 4Å: Chain C: I.38, P.39, S.42, I.136, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain E: N.54, L.57, N.58, Q.64, M.67, Q.68, L.70, K.71, I.74, N.75, A.106, G.107, T.108, Y.131 23 PLIP interactions: 17 interactions with chain E, 6 interactions with chain C Hydrophobic interactions: E:L.57, E:L.57, E:K.71, C:I.38, C:Y.170, C:Y.170 Hydrogen bonds: E:N.54, E:N.58, E:N.58, E:K.71, E:N.75, E:T.108, C:N.184 Water bridges: E:Q.68, E:Q.68, E:N.75 pi-Cation interactions: E:K.71, E:K.71, E:K.71 Halogen bonds: E:K.71, E:N.75, C:Y.170, C:R.174 Y05.18: 24 residues within 4Å: Chain A: I.38, P.39, S.42, I.136, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain F: N.54, L.57, N.58, Q.64, M.67, Q.68, L.70, K.71, I.74, N.75, A.106, G.107, T.108, Y.131 23 PLIP interactions: 17 interactions with chain F, 6 interactions with chain A Hydrophobic interactions: F:L.57, F:L.57, F:K.71, A:I.38, A:Y.170, A:Y.170 Hydrogen bonds: F:N.54, F:N.58, F:N.58, F:K.71, F:N.75, F:T.108, A:N.184 Water bridges: F:Q.68, F:Q.68, F:N.75 pi-Cation interactions: F:K.71, F:K.71, F:K.71 Halogen bonds: F:K.71, F:N.75, A:Y.170, A:R.174

Links

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Citation

Gillis, E.P. et al., Potent Long-Acting Inhibitors Targeting the HIV-1 Capsid Based on a Versatile Quinazolin-4-one Scaffold. J.Med.Chem. (2023)

Release Date

2023-02-15

Peptides

HIV-1 capsid: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

C
C

D
C

E
C

F
C

HIV-1 capsid

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