SMTL ID : 6vkv.2 (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: 26 residues within 4Å: Chain A: 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: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Ligands: CL.5, CL.8 18 PLIP interactions: 3 interactions with chain F, 15 interactions with chain A Hydrogen bonds: F:Q.179, F:N.183, A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 Halogen bonds: F:R.173, A:K.70, A:N.74 Hydrophobic interactions: A:N.53, A:L.56, A:L.56, A:Q.63, A:T.107 Water bridges: A:Q.67 pi-Cation interactions: A:K.70, A:K.70 QNG.9: 26 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 D: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Ligands: CL.13, CL.16 18 PLIP interactions: 15 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:N.53, B:L.56, B:L.56, B:Q.63, B:T.107 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74, D:Q.179, D:N.183 Water bridges: B:Q.67 pi-Cation interactions: B:K.70, B:K.70 Halogen bonds: B:K.70, B:N.74, D:R.173 QNG.17: 26 residues within 4Å: Chain C: 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, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Ligands: CL.21, CL.24 18 PLIP interactions: 15 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:N.53, C:L.56, C:L.56, C:Q.63, C:T.107 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74, E:Q.179, E:N.183 Water bridges: C:Q.67 pi-Cation interactions: C:K.70, C:K.70 Halogen bonds: C:K.70, C:N.74, E:R.173 QNG.25: 26 residues within 4Å: Chain C: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 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 Ligands: CL.29, CL.32 18 PLIP interactions: 15 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:N.53, D:L.56, D:L.56, D:Q.63, D:T.107 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74, C:Q.179, C:N.183 Water bridges: D:Q.67 pi-Cation interactions: D:K.70, D:K.70 Halogen bonds: D:K.70, D:N.74, C:R.173 QNG.33: 26 residues within 4Å: Chain A: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 Chain E: 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 Ligands: CL.37, CL.40 18 PLIP interactions: 3 interactions with chain A, 15 interactions with chain E Hydrogen bonds: A:Q.179, A:N.183, E:N.57, E:N.57, E:K.70, E:N.74, E:N.74 Halogen bonds: A:R.173, E:K.70, E:N.74 Hydrophobic interactions: E:N.53, E:L.56, E:L.56, E:Q.63, E:T.107 Water bridges: E:Q.67 pi-Cation interactions: E:K.70, E:K.70 QNG.41: 26 residues within 4Å: Chain B: I.37, P.38, S.41, I.135, Y.169, L.172, R.173, Q.179, K.182, N.183 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 Ligands: CL.45, CL.48 18 PLIP interactions: 15 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:N.53, F:L.56, F:L.56, F:Q.63, F:T.107 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74, B:Q.179, B:N.183 Water bridges: F:Q.67 pi-Cation interactions: F:K.70, F:K.70 Halogen bonds: F:K.70, F:N.74, B:R.173

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.10: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.18: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.26: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.34: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP

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

CL.3: 2 residues within 4Å: Chain A: L.172, E.175 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.162, M.215 Chain E: M.144 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain A: Q.50, N.53, G.106, Q.114 Ligands: QNG.1 Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain E: P.17, R.18 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: Q.63 Chain F: K.170 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Ligands: QNG.1 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: L.172, E.175 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.162, M.215 Chain F: M.144 Ligand excluded by PLIP CL.13: 5 residues within 4Å: Chain B: Q.50, N.53, G.106, Q.114 Ligands: QNG.9 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain B: Q.63 Chain D: K.170 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Ligands: QNG.9 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: L.172, E.175 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: R.162, M.215 Chain D: M.144 Ligand excluded by PLIP CL.21: 5 residues within 4Å: Chain C: Q.50, N.53, G.106, Q.114 Ligands: QNG.17 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain C: Q.63 Chain E: K.170 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Ligands: QNG.17 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain D: L.172, E.175 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: M.144 Chain D: R.162, M.215 Ligand excluded by PLIP CL.29: 5 residues within 4Å: Chain D: Q.50, N.53, G.106, Q.114 Ligands: QNG.25 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain C: K.170 Chain D: Q.63 Ligand excluded by PLIP CL.32: 1 residues within 4Å: Ligands: QNG.25 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain E: L.172, E.175 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain C: M.144 Chain E: R.162, M.215 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain E: Q.50, N.53, G.106, Q.114 Ligands: QNG.33 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain C: P.17, R.18 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain A: K.170 Chain E: Q.63 Ligand excluded by PLIP CL.40: 1 residues within 4Å: Ligands: QNG.33 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain F: L.172, E.175 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain A: M.144 Chain F: R.162, M.215 Ligand excluded by PLIP CL.45: 5 residues within 4Å: Chain F: Q.50, N.53, G.106, Q.114 Ligands: QNG.41 Ligand excluded by PLIP CL.46: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain B: K.170 Chain F: Q.63 Ligand excluded by PLIP CL.48: 1 residues within 4Å: Ligands: QNG.41 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
C

B
C

C
C

D
C

E
C

F
C

Capsid protein p24

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