SMTL ID : 8qv4.1

Hexameric HIV-1 CA in complex with DDD01728503

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.76, E.79, W.80, W.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.76, A:E.76 EDO.2: 5 residues within 4Å: Chain A: M.96, R.97, E.113, G.116, W.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.97, A:W.117 EDO.4: 4 residues within 4Å: Chain B: E.76, E.79, W.80, W.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.76, B:E.76 EDO.5: 5 residues within 4Å: Chain B: M.96, R.97, E.113, G.116, W.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.97, B:W.117 EDO.7: 4 residues within 4Å: Chain C: E.76, E.79, W.80, W.133 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.76, C:E.76 EDO.8: 5 residues within 4Å: Chain C: M.96, R.97, E.113, G.116, W.117 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.97, C:W.117 EDO.10: 4 residues within 4Å: Chain D: E.76, E.79, W.80, W.133 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.76, D:E.76 EDO.11: 5 residues within 4Å: Chain D: M.96, R.97, E.113, G.116, W.117 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.97, D:W.117 EDO.13: 4 residues within 4Å: Chain E: E.76, E.79, W.80, W.133 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.76, E:E.76 EDO.14: 5 residues within 4Å: Chain E: M.96, R.97, E.113, G.116, W.117 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.97, E:W.117 EDO.16: 4 residues within 4Å: Chain F: E.76, E.79, W.80, W.133 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.76, F:E.76 EDO.17: 5 residues within 4Å: Chain F: M.96, R.97, E.113, G.116, W.117 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.97, F:W.117

6 x WZX: ethyl 2-(3-oxidanylidene-2,4-dihydroquinoxalin-1-yl)ethanoate(Non-covalent)

WZX.3: 11 residues within 4Å: Chain A: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.56, A:L.69, A:K.70, A:I.73 Hydrogen bonds: A:N.57, A:N.57 WZX.6: 11 residues within 4Å: Chain B: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.56, B:L.69, B:K.70, B:I.73 Hydrogen bonds: B:N.57, B:N.57 WZX.9: 11 residues within 4Å: Chain C: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.56, C:L.69, C:K.70, C:I.73 Hydrogen bonds: C:N.57, C:N.57 WZX.12: 11 residues within 4Å: Chain D: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.56, D:L.69, D:K.70, D:I.73 Hydrogen bonds: D:N.57, D:N.57 WZX.15: 11 residues within 4Å: Chain E: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:L.56, E:L.69, E:K.70, E:I.73 Hydrogen bonds: E:N.57, E:N.57 WZX.18: 11 residues within 4Å: Chain F: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, A.105, T.107, Y.130 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:L.56, F:L.69, F:K.70, F:I.73 Hydrogen bonds: F:N.57, F:N.57

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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