SMTL ID : 7snn.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-(difluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-yl)acetamide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.37 Å

Oligo State

homo-hexamer

Ligands

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

IOD.1: 1 residues within 4Å: Chain F: P.38 Ligand excluded by PLIP 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 A: P.17 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain D: P.38 Ligand excluded by PLIP IOD.13: 4 residues within 4Å: Chain B: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain B: P.17 Ligand excluded by PLIP IOD.23: 1 residues within 4Å: Chain E: P.38 Ligand excluded by PLIP IOD.24: 4 residues within 4Å: Chain C: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.25: 1 residues within 4Å: Chain C: P.17 Ligand excluded by PLIP IOD.34: 1 residues within 4Å: Chain C: P.38 Ligand excluded by PLIP IOD.35: 4 residues within 4Å: Chain D: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.36: 1 residues within 4Å: Chain D: P.17 Ligand excluded by PLIP IOD.45: 1 residues within 4Å: Chain A: P.38 Ligand excluded by PLIP IOD.46: 4 residues within 4Å: Chain E: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.47: 1 residues within 4Å: Chain E: P.17 Ligand excluded by PLIP IOD.56: 1 residues within 4Å: Chain B: P.38 Ligand excluded by PLIP IOD.57: 4 residues within 4Å: Chain F: G.156, P.157, K.158, E.159 Ligand excluded by PLIP IOD.58: 1 residues within 4Å: Chain F: P.17 Ligand excluded by PLIP

6 x 9WW: N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-methyl-1H-indazol-7-yl}-4-oxo-3,4-dihydroquinazolin-2-yl)-2-(3,5-difluorophenyl)ethyl]-2-[(3aM)-3-(difluoromethyl)cyclopenta[c]pyrazol-1(2H)-yl]acetamide(Non-covalent)

9WW.4: 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 F: L.172, R.173 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:N.53, A:L.56, A:L.56, A:M.66, A:K.70, A:A.105 Hydrogen bonds: A:N.57, A:N.57, A:K.70, A:N.74, A:N.74 pi-Cation interactions: A:K.70, A:K.70 Halogen bonds: A:K.70, A:N.74 9WW.15: 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 D: L.172, R.173 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:N.53, B:L.56, B:L.56, B:M.66, 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:Q.67 pi-Cation interactions: B:K.70, B:K.70 Halogen bonds: B:K.70, B:N.74 9WW.26: 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 E: L.172, R.173 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:N.53, C:L.56, C:L.56, C:M.66, C:K.70, C:A.105 Hydrogen bonds: C:N.57, C:N.57, C:K.70, C:N.74, C:N.74 pi-Cation interactions: C:K.70, C:K.70 Halogen bonds: C:K.70, C:N.74 9WW.37: 16 residues within 4Å: Chain C: 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 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:N.53, D:L.56, D:L.56, D:M.66, D:K.70, D:A.105 Hydrogen bonds: D:N.57, D:N.57, D:K.70, D:N.74, D:N.74 pi-Cation interactions: D:K.70, D:K.70 Halogen bonds: D:K.70, D:N.74 9WW.48: 16 residues within 4Å: Chain A: 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 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:N.53, E:L.56, E:L.56, E:M.66, 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:Q.67 pi-Cation interactions: E:K.70, E:K.70 Halogen bonds: E:K.70, E:N.74 9WW.59: 16 residues within 4Å: Chain B: 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 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:N.53, F:L.56, F:L.56, F:M.66, F:K.70, F:A.105 Hydrogen bonds: F:N.57, F:N.57, F:K.70, F:N.74, F:N.74 pi-Cation interactions: F:K.70, F:K.70 Halogen bonds: F:K.70, F:N.74

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

CL.5: 4 residues within 4Å: Chain A: G.61 Chain F: E.35, K.170, R.173 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: P.160, F.161, R.162 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: I.153, R.167 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: E.28, G.60, H.62 Ligand excluded by PLIP CL.9: 1 residues within 4Å: Chain A: I.124 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: P.17, R.18 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: R.162, M.215, Q.219 Chain E: M.144 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: G.61 Chain D: E.35, K.170, R.173 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: P.160, F.161, R.162 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain B: I.153, R.167 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: E.28, G.60, H.62 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: I.124 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: P.17, R.18 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: R.162, M.215, Q.219 Chain F: M.144 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain C: G.61 Chain E: E.35, K.170, R.173 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: P.160, F.161, R.162 Ligand excluded by PLIP CL.29: 2 residues within 4Å: Chain C: I.153, R.167 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain C: E.28, G.60, H.62 Ligand excluded by PLIP CL.31: 1 residues within 4Å: Chain C: I.124 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain C: P.17, R.18 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain C: R.162, M.215, Q.219 Chain D: M.144 Ligand excluded by PLIP CL.38: 4 residues within 4Å: Chain C: E.35, K.170, R.173 Chain D: G.61 Ligand excluded by PLIP CL.39: 3 residues within 4Å: Chain D: P.160, F.161, R.162 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain D: I.153, R.167 Ligand excluded by PLIP CL.41: 3 residues within 4Å: Chain D: E.28, G.60, H.62 Ligand excluded by PLIP CL.42: 1 residues within 4Å: Chain D: I.124 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain D: P.17, R.18 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain B: M.144 Chain D: R.162, M.215, Q.219 Ligand excluded by PLIP CL.49: 4 residues within 4Å: Chain A: E.35, K.170, R.173 Chain E: G.61 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain E: P.160, F.161, R.162 Ligand excluded by PLIP CL.51: 2 residues within 4Å: Chain E: I.153, R.167 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain E: E.28, G.60, H.62 Ligand excluded by PLIP CL.53: 1 residues within 4Å: Chain E: I.124 Ligand excluded by PLIP CL.54: 2 residues within 4Å: Chain E: P.17, R.18 Ligand excluded by PLIP CL.55: 4 residues within 4Å: Chain C: M.144 Chain E: R.162, M.215, Q.219 Ligand excluded by PLIP CL.60: 4 residues within 4Å: Chain B: E.35, K.170, R.173 Chain F: G.61 Ligand excluded by PLIP CL.61: 3 residues within 4Å: Chain F: P.160, F.161, R.162 Ligand excluded by PLIP CL.62: 2 residues within 4Å: Chain F: I.153, R.167 Ligand excluded by PLIP CL.63: 3 residues within 4Å: Chain F: E.28, G.60, H.62 Ligand excluded by PLIP CL.64: 1 residues within 4Å: Chain F: I.124 Ligand excluded by PLIP CL.65: 2 residues within 4Å: Chain F: P.17, R.18 Ligand excluded by PLIP CL.66: 4 residues within 4Å: Chain A: M.144 Chain F: R.162, M.215, Q.219 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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-(difluoromethyl)-5,6-dihydrocyclopenta[c]pyrazol-1(4H)-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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