SMTL ID : 7rmj.1 (1 other biounit)

Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor (S)-N-(1-(3-(4-chloro-3-(methylsulfonamido)-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-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

homo-hexamer

Ligands

6 x 61F: N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl}-6-[3-(methanesulfonyl)-3-methylbut-1-yn-1-yl]pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl]acetamide(Non-covalent)

61F.1: 19 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, T.107, Y.130 Chain F: I.37, P.38, S.41, Y.169, L.172, R.173 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:L.56, A:L.56, A:Q.67, A:T.107, F:P.38, F:Y.169 Hydrogen bonds: A:N.57, A:N.57, A:K.70, A:N.74 pi-Cation interactions: A:K.70, A:K.70 Halogen bonds: A:K.70, A:N.74, F:Y.169 61F.8: 21 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, T.107, Y.130 Chain E: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:L.56, B:L.56, B:Q.67, B:K.70, B:T.107, E:P.38, E:Y.169 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74 pi-Cation interactions: B:K.70 Halogen bonds: B:K.70, B:N.74, E:Y.169 61F.16: 19 residues within 4Å: Chain B: I.37, P.38, S.41, Y.169, L.172, R.173 Chain C: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 15 PLIP interactions: 12 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.56, C:L.56, C:Q.67, C:T.107, B:P.38, B:Y.169 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74 pi-Cation interactions: C:K.70, C:K.70 Halogen bonds: C:K.70, C:N.74, B:Y.169 61F.23: 21 residues within 4Å: Chain A: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain D: N.53, 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: 13 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:L.56, D:L.56, D:Q.67, D:K.70, D:T.107, A:P.38, A:Y.169 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74 pi-Cation interactions: D:K.70 Halogen bonds: D:K.70, D:N.74, A:Y.169 61F.31: 19 residues within 4Å: Chain D: I.37, P.38, S.41, Y.169, L.172, R.173 Chain E: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 15 PLIP interactions: 12 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.56, E:L.56, E:Q.67, E:T.107, D:P.38, D:Y.169 Hydrogen bonds: E:N.57, E:N.57, E:K.70, E:N.74 pi-Cation interactions: E:K.70, E:K.70 Halogen bonds: E:K.70, E:N.74, D:Y.169 61F.38: 21 residues within 4Å: Chain C: I.37, P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain F: N.53, 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: 13 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: F:L.56, F:L.56, F:Q.67, F:K.70, F:T.107, C:P.38, C:Y.169 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74 pi-Cation interactions: F:K.70 Halogen bonds: F:K.70, F:N.74, C:Y.169

9 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.9: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: R.18 Chain C: P.17 Ligand excluded by PLIP IOD.17: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 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.25: 2 residues within 4Å: Chain D: R.18 Chain E: P.17 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.40: 2 residues within 4Å: Chain A: P.17 Chain F: R.18 Ligand excluded by PLIP

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

CL.3: 2 residues within 4Å: Chain A: Q.63 Chain F: E.35 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: Q.50, N.53, G.106 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: M.215, Q.219 Chain D: M.144 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: P.17, R.18 Chain F: R.18 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain D: P.17 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: Q.50, N.53, G.106 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: R.162, M.215, Q.219 Chain C: M.144 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: G.61, Q.63 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: L.6 Chain F: N.5, L.6 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: E.35 Chain C: Q.63 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain C: Q.50, N.53, G.106 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: M.215, Q.219 Chain F: M.144 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: R.18 Chain C: P.17, R.18 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain F: P.17 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain D: Q.50, N.53, G.106 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain D: R.162, M.215, Q.219 Chain E: M.144 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain D: G.61, Q.63 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain B: N.5, L.6 Chain E: L.6 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain D: E.35 Chain E: Q.63 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain E: Q.50, N.53, G.106 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain B: M.144 Chain E: M.215, Q.219 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: R.18 Chain E: P.17, R.18 Ligand excluded by PLIP CL.37: 1 residues within 4Å: Chain B: P.17 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain F: Q.50, N.53, G.106 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain A: M.144 Chain F: R.162, M.215, Q.219 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain F: G.61, Q.63 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain A: L.6 Chain D: N.5, L.6 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bester, S.M. et al., Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir. Mbio (2022)

Release Date

2022-08-03

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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