SMTL ID : 8qux.1

Hexameric HIV-1 CA in complex with DDD00100333

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: E.76, E.79, W.80, R.132, W.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.76, A:W.80, A:R.132 EDO.3: 7 residues within 4Å: Chain A: I.73, N.74, A.77, S.102, A.105, T.107 Ligands: S0I.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.107, A:T.107 EDO.4: 5 residues within 4Å: Chain B: E.76, E.79, W.80, R.132, W.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.76, B:W.80, B:R.132 EDO.6: 7 residues within 4Å: Chain B: I.73, N.74, A.77, S.102, A.105, T.107 Ligands: S0I.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.107, B:T.107 EDO.7: 5 residues within 4Å: Chain C: E.76, E.79, W.80, R.132, W.133 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.76, C:W.80, C:R.132 EDO.9: 7 residues within 4Å: Chain C: I.73, N.74, A.77, S.102, A.105, T.107 Ligands: S0I.8 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.107, C:T.107 EDO.10: 5 residues within 4Å: Chain D: E.76, E.79, W.80, R.132, W.133 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.76, D:W.80, D:R.132 EDO.12: 7 residues within 4Å: Chain D: I.73, N.74, A.77, S.102, A.105, T.107 Ligands: S0I.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.107, D:T.107 EDO.13: 5 residues within 4Å: Chain E: E.76, E.79, W.80, R.132, W.133 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.76, E:W.80, E:R.132 EDO.15: 7 residues within 4Å: Chain E: I.73, N.74, A.77, S.102, A.105, T.107 Ligands: S0I.14 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:T.107, E:T.107 EDO.16: 5 residues within 4Å: Chain F: E.76, E.79, W.80, R.132, W.133 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.76, F:W.80, F:R.132 EDO.18: 7 residues within 4Å: Chain F: I.73, N.74, A.77, S.102, A.105, T.107 Ligands: S0I.17 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.107, F:T.107

6 x S0I: 4-benzyl-3,4-dihydroquinoxalin-2(1H)-one(Non-covalent)

S0I.2: 12 residues within 4Å: Chain A: N.53, L.56, N.57, M.66, K.70, I.73, N.74, A.105, T.107, Y.130 Chain E: Q.179 Ligands: EDO.3 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:L.56, A:L.56, 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 pi-Cation interactions: A:K.70 S0I.5: 12 residues within 4Å: Chain B: N.53, L.56, N.57, M.66, K.70, I.73, N.74, A.105, T.107, Y.130 Chain F: Q.179 Ligands: EDO.6 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:L.56, B:L.56, 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 pi-Cation interactions: B:K.70 S0I.8: 12 residues within 4Å: Chain C: N.53, L.56, N.57, M.66, K.70, I.73, N.74, A.105, T.107, Y.130 Chain D: Q.179 Ligands: EDO.9 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:Q.179, C:L.56, C:L.56, C:K.70, C:K.70, C:I.73, C:I.73, C:T.107 Hydrogen bonds: C:N.57, C:N.57 pi-Cation interactions: C:K.70 S0I.11: 12 residues within 4Å: Chain B: Q.179 Chain D: N.53, L.56, N.57, M.66, K.70, I.73, N.74, A.105, T.107, Y.130 Ligands: EDO.12 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:L.56, D:L.56, 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 pi-Cation interactions: D:K.70 S0I.14: 12 residues within 4Å: Chain C: Q.179 Chain E: N.53, L.56, N.57, M.66, K.70, I.73, N.74, A.105, T.107, Y.130 Ligands: EDO.15 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:L.56, E:L.56, E:K.70, E:K.70, E:I.73, E:I.73, E:T.107, C:Q.179 Hydrogen bonds: E:N.57, E:N.57 pi-Cation interactions: E:K.70 S0I.17: 12 residues within 4Å: Chain A: Q.179 Chain F: N.53, L.56, N.57, M.66, K.70, I.73, N.74, A.105, T.107, Y.130 Ligands: EDO.18 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain F Hydrophobic interactions: A:Q.179, F:L.56, F:L.56, F:K.70, F:K.70, F:I.73, F:I.73, F:T.107 Hydrogen bonds: F:N.57, F:N.57 pi-Cation interactions: 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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