SMTL ID : 8quk.1

Hexameric HIV-1 CA in complex with DDD00100439

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.76 EDO.2: 4 residues within 4Å: Chain A: W.80, H.84, E.98, P.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.84 EDO.4: 4 residues within 4Å: Chain B: E.76, E.79, W.80, W.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76 EDO.5: 4 residues within 4Å: Chain B: W.80, H.84, E.98, P.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.84 EDO.7: 4 residues within 4Å: Chain C: E.76, E.79, W.80, W.133 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.76 EDO.8: 4 residues within 4Å: Chain C: W.80, H.84, E.98, P.99 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.84 EDO.10: 4 residues within 4Å: Chain D: E.76, E.79, W.80, W.133 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.76 EDO.11: 4 residues within 4Å: Chain D: W.80, H.84, E.98, P.99 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.84 EDO.13: 4 residues within 4Å: Chain E: E.76, E.79, W.80, W.133 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.76 EDO.14: 4 residues within 4Å: Chain E: W.80, H.84, E.98, P.99 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.84 EDO.16: 4 residues within 4Å: Chain F: E.76, E.79, W.80, W.133 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.76 EDO.17: 4 residues within 4Å: Chain F: W.80, H.84, E.98, P.99 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.84

6 x WVU: (phenylmethyl) 3-oxidanylidenepiperazine-1-carboxylate(Non-covalent)

WVU.3: 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 Chain F: Q.179 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:L.56, A:L.56, A:M.66, A:L.69, A:K.70 Hydrogen bonds: A:N.74, A:N.74 Water bridges: A:N.57, A:K.70, F:N.183 pi-Cation interactions: A:K.70 WVU.6: 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 Chain D: Q.179 11 PLIP interactions: 1 interactions with chain D, 10 interactions with chain B Water bridges: D:N.183, B:N.57, B:K.70 Hydrophobic interactions: B:L.56, B:L.56, B:M.66, B:L.69, B:K.70 Hydrogen bonds: B:N.74, B:N.74 pi-Cation interactions: B:K.70 WVU.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 Chain E: Q.179 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:L.56, C:L.56, C:M.66, C:L.69, C:K.70 Hydrogen bonds: C:N.74, C:N.74 Water bridges: C:N.57, C:K.70, E:N.183 pi-Cation interactions: C:K.70 WVU.12: 11 residues within 4Å: Chain C: Q.179 Chain D: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 11 PLIP interactions: 1 interactions with chain C, 10 interactions with chain D Water bridges: C:N.183, D:N.57, D:K.70 Hydrophobic interactions: D:L.56, D:L.56, D:M.66, D:L.69, D:K.70 Hydrogen bonds: D:N.74, D:N.74 pi-Cation interactions: D:K.70 WVU.15: 11 residues within 4Å: Chain A: Q.179 Chain E: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain E Water bridges: A:N.183, E:N.57, E:K.70 Hydrophobic interactions: E:L.56, E:L.56, E:M.66, E:L.69, E:K.70 Hydrogen bonds: E:N.74, E:N.74 pi-Cation interactions: E:K.70 WVU.18: 11 residues within 4Å: Chain B: Q.179 Chain F: N.53, L.56, N.57, M.66, L.69, K.70, I.73, N.74, T.107, Y.130 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:L.56, F:L.56, F:M.66, F:L.69, F:K.70 Hydrogen bonds: F:N.74, F:N.74 Water bridges: F:N.57, F:K.70, B:N.183 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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