SMTL ID : 6vkv.1 (1 other biounit)

Co-crystal structure of GS-6207 bound to HIV-1 capsid hexamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 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: 22 residues within 4Å: Chain A: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain D: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 16 PLIP interactions: 14 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:L.56, A:Q.63, A:K.70, A:A.105, A:T.107, D:Y.169 Hydrogen bonds: A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 pi-Cation interactions: A:K.70, A:K.70 Halogen bonds: A:K.70, A:N.74, D:Y.169 QNG.9: 22 residues within 4Å: Chain B: N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain C: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:L.56, B:L.56, B:Q.63, B:M.66, B:K.70, B:K.70, B:A.105, B:T.107, C:P.38 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74, C:Q.179 pi-Cation interactions: B:K.70 Halogen bonds: B:K.70, B:N.74, C:Y.169, C:K.182 QNG.15: 22 residues within 4Å: Chain C: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain F: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 16 PLIP interactions: 2 interactions with chain F, 14 interactions with chain C Hydrophobic interactions: F:Y.169, C:L.56, C:Q.63, C:K.70, C:A.105, C:T.107 Halogen bonds: F:Y.169, C:K.70, C:N.74 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74 pi-Cation interactions: C:K.70, C:K.70 QNG.23: 22 residues within 4Å: Chain D: N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain E: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 20 PLIP interactions: 16 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:L.56, D:L.56, D:Q.63, D:M.66, D:K.70, D:K.70, D:A.105, D:T.107, E:P.38 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74, E:Q.179 pi-Cation interactions: D:K.70 Halogen bonds: D:K.70, D:N.74, E:Y.169, E:K.182 QNG.29: 22 residues within 4Å: Chain B: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain E: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain B Hydrophobic interactions: E:L.56, E:Q.63, E:K.70, E:A.105, E:T.107, B:Y.169 Hydrogen bonds: E:N.57, E:N.57, E:K.70, E:N.74, E:N.74 pi-Cation interactions: E:K.70, E:K.70 Halogen bonds: E:K.70, E:N.74, B:Y.169 QNG.37: 22 residues within 4Å: Chain A: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain F: N.53, T.54, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 20 PLIP interactions: 4 interactions with chain A, 16 interactions with chain F Hydrophobic interactions: A:P.38, F:L.56, F:L.56, F:Q.63, F:M.66, F:K.70, F:K.70, F:A.105, F:T.107 Hydrogen bonds: A:Q.179, F:N.57, F:N.57, F:K.70, F:N.74, F:N.74 Halogen bonds: A:Y.169, A:K.182, F:K.70, F:N.74 pi-Cation interactions: F:K.70

12 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.3: 2 residues within 4Å: Chain A: P.17 Chain D: R.18 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: R.18 Chain F: P.17, R.18, N.21 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.16: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.17: 2 residues within 4Å: Chain C: P.17 Chain F: R.18 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain B: P.17, R.18, N.21 Chain C: R.18 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.30: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.31: 2 residues within 4Å: Chain B: R.18 Chain E: P.17 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain D: P.17, R.18, N.21 Chain E: R.18 Ligand excluded by PLIP IOD.38: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP

24 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: G.61, Q.63 Chain D: E.35, K.170 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: Q.50, N.53, G.106, Q.114 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: R.162, M.215, Q.219 Chain F: M.144 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: P.17, R.18 Chain D: R.18 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: Q.50, N.53, G.106, Q.114 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: R.162, M.215, Q.219 Chain E: M.144 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: G.61, Q.63 Chain C: R.173 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: P.17, R.18 Chain C: R.18 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain C: G.61, Q.63 Chain F: E.35, K.170 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain C: Q.50, N.53, G.106, Q.114 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: M.144 Chain C: R.162, M.215, Q.219 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: P.17, R.18 Chain F: R.18 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain D: Q.50, N.53, G.106, Q.114 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: M.144 Chain D: R.162, M.215, Q.219 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain D: G.61, Q.63 Chain E: R.173 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain D: P.17, R.18 Chain E: R.18 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain B: E.35, K.170 Chain E: G.61, Q.63 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain E: Q.50, N.53, G.106, Q.114 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain D: M.144 Chain E: R.162, M.215, Q.219 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain B: R.18 Chain E: P.17, R.18 Ligand excluded by PLIP CL.39: 4 residues within 4Å: Chain F: Q.50, N.53, G.106, Q.114 Ligand excluded by PLIP CL.40: 4 residues within 4Å: Chain C: M.144 Chain F: R.162, M.215, Q.219 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain A: R.173 Chain F: G.61, Q.63 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain A: R.18 Chain F: P.17, R.18 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bester, S.M. et al., Structural and mechanistic bases for a potent HIV-1 capsid inhibitor. Science (2020)

Release Date

2020-10-21

Peptides

Capsid protein p24: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Capsid protein p24

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