SMTL ID : 7rj2.1

Co-crystal structure of lenacapavir bound to Q67H/N74D mutant of disulfide stabilized HIV-1 CA hexamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 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: 20 residues within 4Å: Chain A: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, H.67, L.69, K.70, I.73, D.74, A.105, T.107, Y.130 Chain E: P.38, S.41, Y.169, L.172, R.173 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:L.56, A:L.56, A:Q.63, A:K.70, A:T.107, E:Y.169 Hydrogen bonds: A:N.57, A:N.57, A:K.70, A:D.74 pi-Cation interactions: A:K.70 Halogen bonds: A:K.70, A:D.74, E:Y.169 QNG.7: 20 residues within 4Å: Chain B: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, H.67, L.69, K.70, I.73, D.74, A.105, T.107, Y.130 Chain F: P.38, S.41, Y.169, L.172, R.173 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:L.56, B:L.56, B:Q.63, B:K.70, B:T.107, F:Y.169 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:D.74 pi-Cation interactions: B:K.70 Halogen bonds: B:K.70, B:D.74, F:Y.169 QNG.13: 20 residues within 4Å: Chain C: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, H.67, L.69, K.70, I.73, D.74, A.105, T.107, Y.130 Chain D: P.38, S.41, Y.169, L.172, R.173 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.56, C:L.56, C:Q.63, C:K.70, C:T.107, D:Y.169 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:D.74 pi-Cation interactions: C:K.70 Halogen bonds: C:K.70, C:D.74, D:Y.169 QNG.19: 20 residues within 4Å: Chain B: P.38, S.41, Y.169, L.172, R.173 Chain D: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, H.67, L.69, K.70, I.73, D.74, A.105, T.107, Y.130 14 PLIP interactions: 12 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:L.56, D:L.56, D:Q.63, D:K.70, D:T.107, B:Y.169 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:D.74 pi-Cation interactions: D:K.70 Halogen bonds: D:K.70, D:D.74, B:Y.169 QNG.25: 20 residues within 4Å: Chain C: P.38, S.41, Y.169, L.172, R.173 Chain E: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, H.67, L.69, K.70, I.73, D.74, A.105, T.107, Y.130 14 PLIP interactions: 12 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:L.56, E:L.56, E:Q.63, E:K.70, E:T.107, C:Y.169 Hydrogen bonds: E:N.57, E:N.57, E:K.70, E:D.74 pi-Cation interactions: E:K.70 Halogen bonds: E:K.70, E:D.74, C:Y.169 QNG.31: 20 residues within 4Å: Chain A: P.38, S.41, Y.169, L.172, R.173 Chain F: Q.50, N.53, T.54, L.56, N.57, Q.63, M.66, H.67, L.69, K.70, I.73, D.74, A.105, T.107, Y.130 14 PLIP interactions: 12 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:L.56, F:L.56, F:Q.63, F:K.70, F:T.107, A:Y.169 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:D.74 pi-Cation interactions: F:K.70 Halogen bonds: F:K.70, F:D.74, A:Y.169

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

CL.2: 4 residues within 4Å: Chain A: R.162, M.215, Q.219 Chain F: M.144 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: Q.50, N.53, G.106 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: G.61, Q.63 Chain E: E.35, R.173 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.162, M.215, Q.219 Chain D: M.144 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: Q.50, N.53, G.106 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: G.61, Q.63 Chain F: E.35, R.173 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: R.162, M.215, Q.219 Chain E: M.144 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: Q.50, N.53, G.106 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain E: P.17, R.18 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: G.61, Q.63 Chain D: E.35, R.173 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain C: M.144 Chain D: R.162, M.215, Q.219 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain D: Q.50, N.53, G.106 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain C: P.17, R.18 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain B: E.35, R.173 Chain D: G.61, Q.63 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: M.144 Chain E: R.162, M.215, Q.219 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain E: Q.50, N.53, G.106 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain C: E.35, R.173 Chain E: G.61, Q.63 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain B: M.144 Chain F: R.162, M.215, Q.219 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain F: Q.50, N.53, G.106 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain A: E.35, R.173 Chain F: G.61, Q.63 Ligand excluded by PLIP

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.6: 1 residues within 4Å: Chain A: A.92 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain B: A.92 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain C: A.92 Ligand excluded by PLIP IOD.24: 1 residues within 4Å: Chain D: A.92 Ligand excluded by PLIP IOD.30: 1 residues within 4Å: Chain E: A.92 Ligand excluded by PLIP IOD.36: 1 residues within 4Å: Chain F: A.92 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

2022-07-27

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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