SMTL ID : 7snl.1

Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-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 2.39 Å

Oligo State

homo-hexamer

Ligands

6 x 9VI: N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[3-(trifluoromethyl)-6,7-dihydro-1H-indazol-1-yl]acetamide(Non-covalent)

9VI.1: 16 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, G.106, T.107, Y.130 Chain E: L.172, R.173 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:N.53, A:L.56, A:L.56, A:Q.67, A:K.70, A:K.70, A:A.105 Hydrogen bonds: A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 Water bridges: A:N.53 pi-Cation interactions: A:K.70, A:K.70 Halogen bonds: A:K.70, A:N.74 9VI.13: 16 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, G.106, T.107, Y.130 Chain F: L.172, R.173 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:N.53, B:L.56, B:L.56, B:Q.67, B:K.70, B:K.70, B:A.105 Hydrogen bonds: B:N.57, B:N.57, B:K.70, B:N.74, B:N.74 Water bridges: B:N.53 pi-Cation interactions: B:K.70, B:K.70 Halogen bonds: B:K.70, B:N.74 9VI.25: 16 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 Chain D: L.172, R.173 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:N.53, C:L.56, C:L.56, C:Q.67, C:K.70, C:K.70, C:A.105 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74 Water bridges: C:N.53 pi-Cation interactions: C:K.70, C:K.70 Halogen bonds: C:K.70, C:N.74 9VI.37: 16 residues within 4Å: Chain B: L.172, R.173 Chain D: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:N.53, D:L.56, D:L.56, D:Q.67, D:K.70, D:K.70, D:A.105 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74 Water bridges: D:N.53 pi-Cation interactions: D:K.70, D:K.70 Halogen bonds: D:K.70, D:N.74 9VI.49: 16 residues within 4Å: Chain C: 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, G.106, T.107, Y.130 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:N.53, E:L.56, E:L.56, E:Q.67, E:K.70, E:K.70, E:A.105 Hydrogen bonds: E:N.57, E:N.57, E:K.70, E:N.74, E:N.74 Water bridges: E:N.53 pi-Cation interactions: E:K.70, E:K.70 Halogen bonds: E:K.70, E:N.74 9VI.61: 16 residues within 4Å: Chain A: L.172, R.173 Chain F: N.53, L.56, N.57, Q.63, M.66, Q.67, L.69, K.70, I.73, N.74, A.105, G.106, T.107, Y.130 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:N.53, F:L.56, F:L.56, F:Q.67, F:K.70, F:K.70, F:A.105 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74 Water bridges: F:N.53 pi-Cation interactions: F:K.70, F:K.70 Halogen bonds: F:K.70, F:N.74

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

IOD.2: 1 residues within 4Å: Chain E: P.38 Ligand excluded by PLIP IOD.3: 4 residues within 4Å: Chain A: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: R.162, M.215, Q.219 Chain F: M.144 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: P.17 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain F: P.38 Ligand excluded by PLIP IOD.15: 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 B: R.162, M.215, Q.219 Chain D: M.144 Ligand excluded by PLIP IOD.17: 1 residues within 4Å: Chain B: P.17 Ligand excluded by PLIP IOD.26: 1 residues within 4Å: Chain D: P.38 Ligand excluded by PLIP IOD.27: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.28: 4 residues within 4Å: Chain C: R.162, M.215, Q.219 Chain E: M.144 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain C: P.17 Ligand excluded by PLIP IOD.38: 1 residues within 4Å: Chain B: P.38 Ligand excluded by PLIP IOD.39: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.40: 4 residues within 4Å: Chain C: M.144 Chain D: R.162, M.215, Q.219 Ligand excluded by PLIP IOD.41: 1 residues within 4Å: Chain D: P.17 Ligand excluded by PLIP IOD.50: 1 residues within 4Å: Chain C: P.38 Ligand excluded by PLIP IOD.51: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.52: 4 residues within 4Å: Chain A: M.144 Chain E: R.162, M.215, Q.219 Ligand excluded by PLIP IOD.53: 1 residues within 4Å: Chain E: P.17 Ligand excluded by PLIP IOD.62: 1 residues within 4Å: Chain A: P.38 Ligand excluded by PLIP IOD.63: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.64: 4 residues within 4Å: Chain B: M.144 Chain F: R.162, M.215, Q.219 Ligand excluded by PLIP IOD.65: 1 residues within 4Å: Chain F: P.17 Ligand excluded by PLIP

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

CL.6: 5 residues within 4Å: Chain A: G.60, G.61 Chain E: E.35, K.170, R.173 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: P.160, F.161, R.162 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: I.153, R.167 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: T.148, D.152 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: E.28, G.60, H.62 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain A: I.124 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: S.16, P.17, R.18 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: G.60, G.61 Chain F: E.35, K.170, R.173 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: P.160, F.161, R.162 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: I.153, R.167 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: T.148, D.152 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: E.28, G.60, H.62 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain B: I.124 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: S.16, P.17, R.18 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain C: G.60, G.61 Chain D: E.35, K.170, R.173 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain C: P.160, F.161, R.162 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain C: I.153, R.167 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain C: T.148, D.152 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain C: E.28, G.60, H.62 Ligand excluded by PLIP CL.35: 1 residues within 4Å: Chain C: I.124 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain C: S.16, P.17, R.18 Ligand excluded by PLIP CL.42: 5 residues within 4Å: Chain B: E.35, K.170, R.173 Chain D: G.60, G.61 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain D: P.160, F.161, R.162 Ligand excluded by PLIP CL.44: 2 residues within 4Å: Chain D: I.153, R.167 Ligand excluded by PLIP CL.45: 2 residues within 4Å: Chain D: T.148, D.152 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain D: E.28, G.60, H.62 Ligand excluded by PLIP CL.47: 1 residues within 4Å: Chain D: I.124 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain D: S.16, P.17, R.18 Ligand excluded by PLIP CL.54: 5 residues within 4Å: Chain C: E.35, K.170, R.173 Chain E: G.60, G.61 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain E: P.160, F.161, R.162 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain E: I.153, R.167 Ligand excluded by PLIP CL.57: 2 residues within 4Å: Chain E: T.148, D.152 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain E: E.28, G.60, H.62 Ligand excluded by PLIP CL.59: 1 residues within 4Å: Chain E: I.124 Ligand excluded by PLIP CL.60: 3 residues within 4Å: Chain E: S.16, P.17, R.18 Ligand excluded by PLIP CL.66: 5 residues within 4Å: Chain A: E.35, K.170, R.173 Chain F: G.60, G.61 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain F: P.160, F.161, R.162 Ligand excluded by PLIP CL.68: 2 residues within 4Å: Chain F: I.153, R.167 Ligand excluded by PLIP CL.69: 2 residues within 4Å: Chain F: T.148, D.152 Ligand excluded by PLIP CL.70: 3 residues within 4Å: Chain F: E.28, G.60, H.62 Ligand excluded by PLIP CL.71: 1 residues within 4Å: Chain F: I.124 Ligand excluded by PLIP CL.72: 3 residues within 4Å: Chain F: S.16, P.17, R.18 Ligand excluded by PLIP

Links

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Citation

Adu-Ampratwum, D. et al., Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor N-(1-(3-(4-chloro-1-methyl-3-(methylsulfonamido)-1H-indazol-7-yl)-4-oxo-3,4-dihydropyrido[2,3-d]pyrimidin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-yl)acetamide. To Be Published

Release Date

2022-10-05

Peptides

Capsid protein p24: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Capsid protein p24

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