SMTL ID : 8quw.1

Hexameric HIV-1 CA in complex with DDD01044153

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-hexamer

Ligands

6 x WZR: (4~{R})-7-oxidanyl-4-phenyl-3,4-dihydro-1~{H}-quinolin-2-one(Non-covalent)

WZR.1: 9 residues within 4Å: Chain A: N.53, L.56, N.57, M.66, K.70, I.73, N.74, Y.130 Ligands: EDO.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.56, A:L.56, A:M.66, A:K.70, A:K.70, A:K.70, A:I.73 Hydrogen bonds: A:N.57, A:N.74, A:N.74 Water bridges: A:K.70, A:K.70 pi-Cation interactions: A:K.70 WZR.3: 9 residues within 4Å: Chain B: N.53, L.56, N.57, M.66, K.70, I.73, N.74, Y.130 Ligands: EDO.4 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.56, B:L.56, B:M.66, B:K.70, B:K.70, B:K.70, B:I.73 Hydrogen bonds: B:N.57, B:N.74, B:N.74 Water bridges: B:K.70, B:K.70 pi-Cation interactions: B:K.70 WZR.5: 9 residues within 4Å: Chain C: N.53, L.56, N.57, M.66, K.70, I.73, N.74, Y.130 Ligands: EDO.6 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:L.56, C:L.56, C:M.66, C:K.70, C:K.70, C:K.70, C:I.73 Hydrogen bonds: C:N.57, C:N.74, C:N.74 Water bridges: C:K.70, C:K.70 pi-Cation interactions: C:K.70 WZR.7: 9 residues within 4Å: Chain D: N.53, L.56, N.57, M.66, K.70, I.73, N.74, Y.130 Ligands: EDO.8 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.56, D:L.56, D:M.66, D:K.70, D:K.70, D:K.70, D:I.73 Hydrogen bonds: D:N.57, D:N.74, D:N.74 Water bridges: D:K.70, D:K.70 pi-Cation interactions: D:K.70 WZR.9: 9 residues within 4Å: Chain E: N.53, L.56, N.57, M.66, K.70, I.73, N.74, Y.130 Ligands: EDO.10 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.56, E:L.56, E:M.66, E:K.70, E:K.70, E:K.70, E:I.73 Hydrogen bonds: E:N.57, E:N.74, E:N.74 Water bridges: E:K.70, E:K.70 pi-Cation interactions: E:K.70 WZR.11: 9 residues within 4Å: Chain F: N.53, L.56, N.57, M.66, K.70, I.73, N.74, Y.130 Ligands: EDO.12 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.56, F:L.56, F:M.66, F:K.70, F:K.70, F:K.70, F:I.73 Hydrogen bonds: F:N.57, F:N.74, F:N.74 Water bridges: F:K.70, F:K.70 pi-Cation interactions: F:K.70

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: N.74, A.77, S.102, A.105, T.107 Ligands: WZR.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.74, A:T.107 Water bridges: A:N.74, A:S.102 EDO.4: 6 residues within 4Å: Chain B: N.74, A.77, S.102, A.105, T.107 Ligands: WZR.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.74, B:T.107 Water bridges: B:N.74, B:S.102 EDO.6: 6 residues within 4Å: Chain C: N.74, A.77, S.102, A.105, T.107 Ligands: WZR.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.74, C:T.107 Water bridges: C:N.74, C:S.102 EDO.8: 6 residues within 4Å: Chain D: N.74, A.77, S.102, A.105, T.107 Ligands: WZR.7 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.74, D:T.107 Water bridges: D:N.74, D:S.102 EDO.10: 6 residues within 4Å: Chain E: N.74, A.77, S.102, A.105, T.107 Ligands: WZR.9 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.74, E:T.107 Water bridges: E:N.74, E:S.102 EDO.12: 6 residues within 4Å: Chain F: N.74, A.77, S.102, A.105, T.107 Ligands: WZR.11 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:N.74, F:T.107 Water bridges: F:N.74, F:S.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lang, S. et al., Application of an NMR/Crystallography Fragment Screening Platform for the Assessment and Rapid Discovery of New HIV-CA Binding Fragments. Chemmedchem (2024)

Release Date

2024-03-27

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

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