SMTL ID : 7rmj.2 (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 Compare

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: 23 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 E: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Ligands: CL.9 16 PLIP interactions: 3 interactions with chain E, 13 interactions with chain A Hydrophobic interactions: E:Y.169, A:L.56, A:L.56, A:Q.67, A:T.107 Hydrogen bonds: E:Q.179, A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 Halogen bonds: E:Y.169, A:K.70, A:N.74 Water bridges: A:Q.67 pi-Cation interactions: A:K.70 61F.11: 23 residues within 4Å: Chain B: 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 Ligands: CL.19 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:L.56, B:L.56, B:Q.67, B:T.107, F:Y.169 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74, F:Q.179 Water bridges: B:Q.67 pi-Cation interactions: B:K.70 Halogen bonds: B:K.70, B:N.74, F:Y.169 61F.21: 23 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 D: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Ligands: CL.29 16 PLIP interactions: 13 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.56, C:L.56, C:Q.67, C:T.107, D:Y.169 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74, D:Q.179 Water bridges: C:Q.67 pi-Cation interactions: C:K.70 Halogen bonds: C:K.70, C:N.74, D:Y.169 61F.31: 23 residues within 4Å: Chain B: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain D: 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 Ligands: CL.39 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:L.56, D:L.56, D:Q.67, D:T.107, B:Y.169 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74, B:Q.179 Water bridges: D:Q.67 pi-Cation interactions: D:K.70 Halogen bonds: D:K.70, D:N.74, B:Y.169 61F.41: 23 residues within 4Å: Chain C: 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 Ligands: CL.49 16 PLIP interactions: 13 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:L.56, E:L.56, E:Q.67, E:T.107, C:Y.169 Hydrogen bonds: E:N.57, E:N.57, E:K.70, E:N.74, E:N.74, C:Q.179 Water bridges: E:Q.67 pi-Cation interactions: E:K.70 Halogen bonds: E:K.70, E:N.74, C:Y.169 61F.51: 23 residues within 4Å: Chain A: P.38, S.41, Y.169, L.172, R.173, Q.179, K.182 Chain F: 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 Ligands: CL.59 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain A Hydrophobic interactions: F:L.56, F:L.56, F:Q.67, F:T.107, A:Y.169 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74, A:Q.179 Water bridges: F:Q.67 pi-Cation interactions: F:K.70 Halogen bonds: F:K.70, F:N.74, A:Y.169

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: 1 residues within 4Å: Chain F: P.17 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain D: P.17 Ligand excluded by PLIP IOD.22: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain E: P.17 Ligand excluded by PLIP IOD.32: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.33: 1 residues within 4Å: Chain C: P.17 Ligand excluded by PLIP IOD.42: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain A: P.17 Ligand excluded by PLIP IOD.52: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.53: 1 residues within 4Å: Chain B: P.17 Ligand excluded by PLIP

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

CL.4: 2 residues within 4Å: Chain A: L.172, E.175 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: R.162, M.215, Q.219 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: Q.50, N.53, G.106 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: G.61, Q.63 Chain E: K.170 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Ligands: 61F.1 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: K.203, P.207 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain B: L.172, E.175 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: R.162, M.215, Q.219 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: Q.50, N.53, G.106 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: G.61, Q.63 Chain F: K.170 Ligand excluded by PLIP CL.19: 1 residues within 4Å: Ligands: 61F.11 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: K.203, P.207 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain C: L.172, E.175 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain C: R.162, M.215, Q.219 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain C: Q.50, N.53, G.106 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain E: P.17, R.18 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: G.61, Q.63 Chain D: K.170 Ligand excluded by PLIP CL.29: 1 residues within 4Å: Ligands: 61F.21 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain C: K.203, P.207 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain D: L.172, E.175 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain D: R.162, M.215, Q.219 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: Q.50, N.53, G.106 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain C: P.17, R.18 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain B: K.170 Chain D: G.61, Q.63 Ligand excluded by PLIP CL.39: 1 residues within 4Å: Ligands: 61F.31 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain D: K.203, P.207 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain E: L.172, E.175 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain E: R.162, M.215, Q.219 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain E: Q.50, N.53, G.106 Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain C: K.170 Chain E: G.61, Q.63 Ligand excluded by PLIP CL.49: 1 residues within 4Å: Ligands: 61F.41 Ligand excluded by PLIP CL.50: 2 residues within 4Å: Chain E: K.203, P.207 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain F: L.172, E.175 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain F: R.162, M.215, Q.219 Ligand excluded by PLIP CL.56: 3 residues within 4Å: Chain F: Q.50, N.53, G.106 Ligand excluded by PLIP CL.57: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain A: K.170 Chain F: G.61, Q.63 Ligand excluded by PLIP CL.59: 1 residues within 4Å: Ligands: 61F.51 Ligand excluded by PLIP CL.60: 2 residues within 4Å: Chain F: K.203, P.207 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
C

B
C

C
C

D
C

E
C

F
C

CAPSID PROTEIN P24

Related Entries With Identical Sequence