SMTL ID : 8qva.1

Hexameric HIV-1 CA in complex with DDD01829894

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: N.74, A.77, S.102, A.105, T.107 Ligands: WZ9.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.107, A:T.107 Water bridges: A:N.74 EDO.2: 4 residues within 4Å: Chain A: E.76, E.79, W.80, W.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.76, A:E.76 Water bridges: A:R.132, A:R.132 EDO.4: 6 residues within 4Å: Chain B: N.74, A.77, S.102, A.105, T.107 Ligands: WZ9.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.107, B:T.107 Water bridges: B:N.74 EDO.5: 4 residues within 4Å: Chain B: E.76, E.79, W.80, W.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.76, B:E.76 Water bridges: B:R.132, B:R.132 EDO.7: 6 residues within 4Å: Chain C: N.74, A.77, S.102, A.105, T.107 Ligands: WZ9.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.107, C:T.107 Water bridges: C:N.74 EDO.8: 4 residues within 4Å: Chain C: E.76, E.79, W.80, W.133 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.76, C:E.76 Water bridges: C:R.132, C:R.132 EDO.10: 6 residues within 4Å: Chain D: N.74, A.77, S.102, A.105, T.107 Ligands: WZ9.12 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.107, D:T.107 Water bridges: D:N.74 EDO.11: 4 residues within 4Å: Chain D: E.76, E.79, W.80, W.133 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.76, D:E.76 Water bridges: D:R.132, D:R.132 EDO.13: 6 residues within 4Å: Chain E: N.74, A.77, S.102, A.105, T.107 Ligands: WZ9.15 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.107, E:T.107 Water bridges: E:N.74 EDO.14: 4 residues within 4Å: Chain E: E.76, E.79, W.80, W.133 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.76, E:E.76 Water bridges: E:R.132, E:R.132 EDO.16: 6 residues within 4Å: Chain F: N.74, A.77, S.102, A.105, T.107 Ligands: WZ9.18 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:T.107, F:T.107 Water bridges: F:N.74 EDO.17: 4 residues within 4Å: Chain F: E.76, E.79, W.80, W.133 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:E.76, F:E.76 Water bridges: F:R.132, F:R.132

6 x WZ9: 7-azanyl-3-(phenylmethyl)-1~{H}-benzimidazol-2-one(Non-covalent)

WZ9.3: 12 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 Chain E: Q.179 Ligands: EDO.1 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.56, A:M.66, A:L.69, A:K.70, A:K.70, A:I.73, A:I.73, A:T.107, E:Q.179 Hydrogen bonds: A:N.57, A:N.57, A:N.57 Water bridges: A:N.53, A:V.59, A:Q.63, A:K.70, A:K.70 WZ9.6: 12 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 Chain F: Q.179 Ligands: EDO.4 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:L.56, B:M.66, B:L.69, B:K.70, B:K.70, B:I.73, B:I.73, B:T.107, F:Q.179 Hydrogen bonds: B:N.57, B:N.57, B:N.57 Water bridges: B:N.53, B:V.59, B:Q.63, B:K.70, B:K.70 WZ9.9: 12 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 Chain D: Q.179 Ligands: EDO.7 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.56, C:M.66, C:L.69, C:K.70, C:K.70, C:I.73, C:I.73, C:T.107, D:Q.179 Hydrogen bonds: C:N.57, C:N.57, C:N.57 Water bridges: C:N.53, C:V.59, C:Q.63, C:K.70, C:K.70 WZ9.12: 12 residues within 4Å: Chain B: Q.179 Chain D: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.10 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.56, D:M.66, D:L.69, D:K.70, D:K.70, D:I.73, D:I.73, D:T.107, B:Q.179 Hydrogen bonds: D:N.57, D:N.57, D:N.57 Water bridges: D:N.53, D:V.59, D:Q.63, D:K.70, D:K.70 WZ9.15: 12 residues within 4Å: Chain C: Q.179 Chain E: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.13 17 PLIP interactions: 1 interactions with chain C, 16 interactions with chain E Hydrophobic interactions: C:Q.179, E:L.56, E:M.66, E:L.69, E:K.70, E:K.70, E:I.73, E:I.73, E:T.107 Hydrogen bonds: E:N.57, E:N.57, E:N.57 Water bridges: E:N.53, E:V.59, E:Q.63, E:K.70, E:K.70 WZ9.18: 12 residues within 4Å: Chain A: Q.179 Chain F: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.16 17 PLIP interactions: 1 interactions with chain A, 16 interactions with chain F Hydrophobic interactions: A:Q.179, F:L.56, F:M.66, F:L.69, F:K.70, F:K.70, F:I.73, F:I.73, F:T.107 Hydrogen bonds: F:N.57, F:N.57, F:N.57 Water bridges: F:N.53, F:V.59, F:Q.63, F:K.70, F:K.70

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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