SMTL ID : 6v2f.3 (2 other biounits)

Crystal structure of the HIV capsid hexamer bound to the small molecule long-acting inhibitor, GS-6207

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x QNG: N-[(1S)-1-(3-{4-chloro-3-[(methylsulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-methyl-3-(methylsulfonyl)but-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3bS,4aR)-5,5-difluoro-3-(trifluoromethyl)-3b,4,4a,5-tetrahydro-1H-cyclopropa[3,4]cyclopenta[1,2-c]pyrazol-1-yl]acetamide(Non-covalent)

QNG.1: 25 residues within 4Å: Chain A: Q.51, N.54, T.55, 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, Y.170, L.173, R.174, Q.180, K.183, N.184 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain D Hydrophobic interactions: A:L.57, A:L.57, A:K.71, A:K.71, A:A.106, A:T.108, D:I.38, D:Y.170, D:Y.170 Hydrogen bonds: A:N.58, A:N.58, A:K.71, A:N.75, D:N.184 pi-Cation interactions: A:K.71, A:K.71, A:K.71 Halogen bonds: A:K.71, D:R.174, D:Q.180 QNG.2: 25 residues within 4Å: Chain A: I.38, P.39, S.42, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain B: Q.51, N.54, T.55, 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 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:I.38, A:Y.170, B:L.57, B:L.57, B:M.67, B:K.71, B:K.71, B:A.106, B:T.108 Hydrogen bonds: A:N.184, B:N.58, B:N.58, B:K.71, B:N.75, B:N.75 Halogen bonds: A:R.174, A:Q.180, B:K.71 pi-Cation interactions: B:K.71, B:K.71, B:K.71 QNG.3: 25 residues within 4Å: Chain C: Q.51, N.54, T.55, 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, Y.170, L.173, R.174, Q.180, K.183, N.184 20 PLIP interactions: 14 interactions with chain C, 6 interactions with chain F Hydrophobic interactions: C:L.57, C:L.57, C:K.71, C:K.71, C:A.106, C:T.108, F:I.38, F:Y.170, F:Y.170 Hydrogen bonds: C:N.58, C:N.58, C:K.71, C:N.75, F:N.184 pi-Cation interactions: C:K.71, C:K.71, C:K.71 Halogen bonds: C:K.71, F:R.174, F:Q.180 QNG.4: 25 residues within 4Å: Chain C: I.38, P.39, S.42, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain D: Q.51, N.54, T.55, 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 21 PLIP interactions: 5 interactions with chain C, 16 interactions with chain D Hydrophobic interactions: C:I.38, C:Y.170, D:L.57, D:L.57, D:M.67, D:K.71, D:K.71, D:A.106, D:T.108 Hydrogen bonds: C:N.184, D:N.58, D:N.58, D:K.71, D:N.75, D:N.75 Halogen bonds: C:R.174, C:Q.180, D:K.71 pi-Cation interactions: D:K.71, D:K.71, D:K.71 QNG.5: 25 residues within 4Å: Chain B: I.38, P.39, S.42, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain E: Q.51, N.54, T.55, 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 20 PLIP interactions: 6 interactions with chain B, 14 interactions with chain E Hydrophobic interactions: B:I.38, B:Y.170, B:Y.170, E:L.57, E:L.57, E:K.71, E:K.71, E:A.106, E:T.108 Hydrogen bonds: B:N.184, E:N.58, E:N.58, E:K.71, E:N.75 Halogen bonds: B:R.174, B:Q.180, E:K.71 pi-Cation interactions: E:K.71, E:K.71, E:K.71 QNG.6: 25 residues within 4Å: Chain E: I.38, P.39, S.42, Y.170, L.173, R.174, Q.180, K.183, N.184 Chain F: Q.51, N.54, T.55, 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 21 PLIP interactions: 16 interactions with chain F, 5 interactions with chain E Hydrophobic interactions: F:L.57, F:L.57, F:M.67, F:K.71, F:K.71, F:A.106, F:T.108, E:I.38, E:Y.170 Hydrogen bonds: F:N.58, F:N.58, F:K.71, F:N.75, F:N.75, E:N.184 pi-Cation interactions: F:K.71, F:K.71, F:K.71 Halogen bonds: F:K.71, E:R.174, E:Q.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Link, J.O. et al., Clinical targeting of HIV capsid protein with a long-acting small molecule. Nature (2020)

Release Date

2020-07-01

Peptides

HIV-1 capsid: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
E

D
F

E
E

F
F

HIV-1 capsid

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