SMTL ID : 8v17.1

HIV-CA Disulfide linked Hexamer with inhibitor bound - exploration of a benzothiazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

6 x Y4X: N-(1,3-benzothiazol-5-yl)-3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-methyl-L-phenylalaninamide(Non-covalent)

Y4X.1: 16 residues within 4Å: Chain A: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain F: Y.169, R.173, K.182 Ligands: GOL.24 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:L.56, A:L.56, A:M.66, F:R.173, F:R.173 Hydrogen bonds: A:N.57, A:N.57, A:Q.63, A:K.70 pi-Cation interactions: A:K.70, A:K.70, A:K.70 Water bridges: F:R.173 Y4X.5: 16 residues within 4Å: Chain B: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain D: Y.169, R.173, K.182 Ligands: GOL.16 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain D Hydrophobic interactions: B:L.56, B:L.56, B:M.66, D:R.173, D:R.173 Hydrogen bonds: B:N.57, B:N.57, B:Q.63, B:K.70 pi-Cation interactions: B:K.70, B:K.70, B:K.70 Water bridges: D:R.173 Y4X.9: 16 residues within 4Å: Chain C: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Chain E: Y.169, R.173, K.182 Ligands: GOL.20 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain E Hydrophobic interactions: C:L.56, C:L.56, C:M.66, E:R.173, E:R.173 Hydrogen bonds: C:N.57, C:N.57, C:Q.63, C:K.70 pi-Cation interactions: C:K.70, C:K.70, C:K.70 Water bridges: E:R.173 Y4X.13: 16 residues within 4Å: Chain C: Y.169, R.173, K.182 Chain D: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Ligands: GOL.12 13 PLIP interactions: 10 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.56, D:L.56, D:M.66, C:R.173, C:R.173 Hydrogen bonds: D:N.57, D:N.57, D:Q.63, D:K.70 pi-Cation interactions: D:K.70, D:K.70, D:K.70 Water bridges: C:R.173 Y4X.17: 16 residues within 4Å: Chain A: Y.169, R.173, K.182 Chain E: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Ligands: GOL.4 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain E Hydrophobic interactions: A:R.173, A:R.173, E:L.56, E:L.56, E:M.66 Water bridges: A:R.173 Hydrogen bonds: E:N.57, E:N.57, E:Q.63, E:K.70 pi-Cation interactions: E:K.70, E:K.70, E:K.70 Y4X.21: 16 residues within 4Å: Chain B: Y.169, R.173, K.182 Chain F: N.53, L.56, N.57, Q.63, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 Ligands: GOL.8 13 PLIP interactions: 10 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:L.56, F:L.56, F:M.66, B:R.173, B:R.173 Hydrogen bonds: F:N.57, F:N.57, F:Q.63, F:K.70 pi-Cation interactions: F:K.70, F:K.70, F:K.70 Water bridges: B:R.173

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: Q.50, D.51, T.54 Chain F: S.41, A.42, C.45 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: H.12, Q.13, C.14 Chain F: I.2, V.3, Q.4, G.46 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: P.34, I.37, P.38, N.139, R.173 Chain E: N.57 Ligands: Y4X.17 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain B: Q.50, D.51, T.54 Chain D: S.41, A.42, C.45 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain B: H.12, Q.13, C.14 Chain D: I.2, V.3, Q.4, G.46 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain B: P.34, I.37, P.38, N.139, R.173 Chain F: N.57 Ligands: Y4X.21 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain C: Q.50, D.51, T.54 Chain E: S.41, A.42, C.45 Ligand excluded by PLIP GOL.11: 7 residues within 4Å: Chain C: H.12, Q.13, C.14 Chain E: I.2, V.3, Q.4, G.46 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain C: P.34, I.37, P.38, N.139, R.173 Chain D: N.57 Ligands: Y4X.13 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain C: S.41, A.42, C.45 Chain D: Q.50, D.51, T.54 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain C: I.2, V.3, Q.4, G.46 Chain D: H.12, Q.13, C.14 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain B: N.57 Chain D: P.34, I.37, P.38, N.139, R.173 Ligands: Y4X.5 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: S.41, A.42, C.45 Chain E: Q.50, D.51, T.54 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain A: I.2, V.3, Q.4, G.46 Chain E: H.12, Q.13, C.14 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain C: N.57 Chain E: P.34, I.37, P.38, N.139, R.173 Ligands: Y4X.9 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: S.41, A.42, C.45 Chain F: Q.50, D.51, T.54 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: I.2, V.3, Q.4, G.46 Chain F: H.12, Q.13, C.14 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain A: N.57 Chain F: P.34, I.37, P.38, N.139, R.173 Ligands: Y4X.1 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, S. et al., Pseudosubstrate Envelope"/Free Energy Perturbation-Guided Design and Mechanistic Investigations of Benzothiazole HIV Capsid Modulators with High Ligand Efficiency. J.Med.Chem. (2024)

Release Date

2024-12-11

Peptides

Spacer peptide 1: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Spacer peptide 1