SMTL ID : 8qv9.1

Hexameric HIV-1 CA in complex with DDD01829021

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-hexamer

Ligands

6 x WZL: 7-bromanyl-3-(phenylmethyl)-1~{H}-benzimidazol-2-one(Non-covalent)

WZL.1: 11 residues within 4Å: Chain A: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.56, A:L.69, A:L.69, A:K.70, A:K.70, A:K.70, A:I.73, A:I.73, A:T.107 Hydrogen bonds: A:N.57, A:N.57 Water bridges: A:N.53 WZL.5: 11 residues within 4Å: Chain B: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.56, B:L.69, B:L.69, B:K.70, B:K.70, B:K.70, B:I.73, B:I.73, B:T.107 Hydrogen bonds: B:N.57, B:N.57 Water bridges: B:N.53 WZL.9: 11 residues within 4Å: Chain C: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.56, C:L.69, C:L.69, C:K.70, C:K.70, C:K.70, C:I.73, C:I.73, C:T.107 Hydrogen bonds: C:N.57, C:N.57 Water bridges: C:N.53 WZL.13: 11 residues within 4Å: Chain D: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.14 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:L.56, D:L.69, D:L.69, D:K.70, D:K.70, D:K.70, D:I.73, D:I.73, D:T.107 Hydrogen bonds: D:N.57, D:N.57 Water bridges: D:N.53 WZL.17: 11 residues within 4Å: Chain E: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.18 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:L.56, E:L.69, E:L.69, E:K.70, E:K.70, E:K.70, E:I.73, E:I.73, E:T.107 Hydrogen bonds: E:N.57, E:N.57 Water bridges: E:N.53 WZL.21: 11 residues within 4Å: Chain F: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.22 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:L.56, F:L.69, F:L.69, F:K.70, F:K.70, F:K.70, F:I.73, F:I.73, F:T.107 Hydrogen bonds: F:N.57, F:N.57 Water bridges: F:N.53

18 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: WZL.1 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: E.76, E.79, W.80, L.83, W.133 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: K.30, A.31, F.32, S.33, Y.145 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain B: N.74, A.77, S.102, A.105, T.107 Ligands: WZL.5 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain B: E.76, E.79, W.80, L.83, W.133 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: K.30, A.31, F.32, S.33, Y.145 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain C: N.74, A.77, S.102, A.105, T.107 Ligands: WZL.9 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain C: E.76, E.79, W.80, L.83, W.133 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: K.30, A.31, F.32, S.33, Y.145 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain D: N.74, A.77, S.102, A.105, T.107 Ligands: WZL.13 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain D: E.76, E.79, W.80, L.83, W.133 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain D: K.30, A.31, F.32, S.33, Y.145 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain E: N.74, A.77, S.102, A.105, T.107 Ligands: WZL.17 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain E: E.76, E.79, W.80, L.83, W.133 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain E: K.30, A.31, F.32, S.33, Y.145 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain F: N.74, A.77, S.102, A.105, T.107 Ligands: WZL.21 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain F: E.76, E.79, W.80, L.83, W.133 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain F: K.30, A.31, F.32, S.33, Y.145 Ligand excluded by PLIP

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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