SMTL ID : 8bds.1

Ternary complex between VCB, BRD4-BD1 and PROTAC 48

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.8, E.91, P.92, F.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.93 Salt bridges: A:R.8 SO4.2: 6 residues within 4Å: Chain A: M.1, D.2, F.4, S.64, R.68 Chain B: R.67 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.2, A:D.2, A:S.64 Water bridges: A:R.68 Salt bridges: A:R.68, B:R.67 SO4.3: 1 residues within 4Å: Chain A: R.9 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.37, A:R.37 Salt bridges: A:R.9 SO4.7: 3 residues within 4Å: Chain C: G.53, T.54, G.55 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.55

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

EDO.4: 5 residues within 4Å: Chain B: I.7, S.8, N.46, F.47, R.48 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain C: E.109, L.112, R.116, D.139, H.140, P.141 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.116, C:R.116 Water bridges: C:D.136, C:N.142, C:D.146 EDO.8: 1 residues within 4Å: Ligands: QIY.6 1 PLIP interactions: 1 interactions with chain D Water bridges: D:L.51 EDO.9: 4 residues within 4Å: Chain D: T.93, Y.96, E.113 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.113 EDO.10: 1 residues within 4Å: Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain D: T.62, M.64, R.72, D.87 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.72, D:R.72 Water bridges: D:D.87, D:D.87, D:D.87, D:D.87

1 x QIY: (2S,4R)-N-[(1S)-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8$l^{5},11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-propyl]-1-[(2R)-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

QIY.6: 25 residues within 4Å: Chain C: R.18, F.25, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: W.40, P.41, F.42, V.46, L.51, L.53, Y.98, N.99, D.104, I.105, M.108 Ligands: EDO.8 28 PLIP interactions: 14 interactions with chain C, 14 interactions with chain D Hydrophobic interactions: C:Y.47, C:Y.47, C:Y.47, C:I.58, C:Y.61, C:W.66, C:W.66, D:W.40, D:W.40, D:F.42, D:V.46, D:L.51, D:L.51, D:L.53, D:Y.98, D:I.105 Hydrogen bonds: C:H.59, C:H.59, C:S.60, C:Y.61, C:H.64, D:N.99, D:N.99, D:D.104, D:D.104 pi-Stacking: C:Y.61 Halogen bonds: C:P.48 Water bridges: D:Y.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krieger, J. et al., Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design. Chemmedchem (2023)

Release Date

2023-02-15

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
Bromodomain-containing protein 4: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Bromodomain-containing protein 4

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