SMTL ID : 8quj.1

Hexameric HIV-1 CA in complex with DDD00100452

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-hexamer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: E.76, E.79, W.80, W.133 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: W.80, H.84, E.98, P.99, I.124 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: Q.50, G.106, S.109, Q.114 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: N.74, A.77, S.102, A.105, T.107 Ligands: WWR.5 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain B: E.76, E.79, W.80, W.133 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain B: W.80, H.84, E.98, P.99, I.124 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain B: Q.50, G.106, S.109, Q.114 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain B: N.74, A.77, S.102, A.105, T.107 Ligands: WWR.10 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain C: E.76, E.79, W.80, W.133 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: W.80, H.84, E.98, P.99, I.124 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: Q.50, G.106, S.109, Q.114 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain C: N.74, A.77, S.102, A.105, T.107 Ligands: WWR.15 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain D: E.76, E.79, W.80, W.133 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain D: W.80, H.84, E.98, P.99, I.124 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain D: Q.50, G.106, S.109, Q.114 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain D: N.74, A.77, S.102, A.105, T.107 Ligands: WWR.20 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain E: E.76, E.79, W.80, W.133 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain E: W.80, H.84, E.98, P.99, I.124 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain E: Q.50, G.106, S.109, Q.114 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain E: N.74, A.77, S.102, A.105, T.107 Ligands: WWR.25 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain F: E.76, E.79, W.80, W.133 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain F: W.80, H.84, E.98, P.99, I.124 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain F: Q.50, G.106, S.109, Q.114 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain F: N.74, A.77, S.102, A.105, T.107 Ligands: WWR.30 Ligand excluded by PLIP

6 x WWR: 3-(phenylmethyl)-1~{H}-imidazol-2-one(Non-covalent)

WWR.5: 10 residues within 4Å: Chain A: N.53, L.56, N.57, K.70, I.73, N.74, T.107, Y.130 Chain F: Q.179 Ligands: EDO.4 8 PLIP interactions: 1 interactions with chain F, 7 interactions with chain A Hydrophobic interactions: F:Q.179, A:K.70, A:K.70, A:I.73, A:T.107 Hydrogen bonds: A:N.57, A:N.57 pi-Cation interactions: A:K.70 WWR.10: 10 residues within 4Å: Chain B: N.53, L.56, N.57, K.70, I.73, N.74, T.107, Y.130 Chain D: Q.179 Ligands: EDO.9 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:K.70, B:K.70, B:I.73, B:T.107, D:Q.179 Hydrogen bonds: B:N.57, B:N.57 pi-Cation interactions: B:K.70 WWR.15: 10 residues within 4Å: Chain C: N.53, L.56, N.57, K.70, I.73, N.74, T.107, Y.130 Chain E: Q.179 Ligands: EDO.14 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:K.70, C:K.70, C:I.73, C:T.107, E:Q.179 Hydrogen bonds: C:N.57, C:N.57 pi-Cation interactions: C:K.70 WWR.20: 10 residues within 4Å: Chain C: Q.179 Chain D: N.53, L.56, N.57, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.19 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.70, D:K.70, D:I.73, D:T.107, C:Q.179 Hydrogen bonds: D:N.57, D:N.57 pi-Cation interactions: D:K.70 WWR.25: 10 residues within 4Å: Chain A: Q.179 Chain E: N.53, L.56, N.57, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.24 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain E Hydrophobic interactions: A:Q.179, E:K.70, E:K.70, E:I.73, E:T.107 Hydrogen bonds: E:N.57, E:N.57 pi-Cation interactions: E:K.70 WWR.30: 10 residues within 4Å: Chain B: Q.179 Chain F: N.53, L.56, N.57, K.70, I.73, N.74, T.107, Y.130 Ligands: EDO.29 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain B Hydrophobic interactions: F:K.70, F:K.70, F:I.73, F:T.107, B:Q.179 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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