SMTL ID : 8bdx.1 (1 other biounit)

Ternary complex between VCB, BRD4-BD2 and PROTAC 48

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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.1: 25 residues within 4Å: Chain A: W.43, P.44, F.45, V.49, A.53, L.54, L.56, C.98, N.102, H.106, E.107, V.108, M.111 Chain D: R.18, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 22 PLIP interactions: 8 interactions with chain A, 14 interactions with chain D Hydrophobic interactions: A:W.43, A:P.44, A:F.45, A:V.49, A:L.54, A:V.108, D:W.37, D:Y.47, D:I.58, D:I.58, D:Y.61, D:W.66 Hydrogen bonds: A:N.102, A:H.106, D:Y.47, D:H.59, D:H.59, D:S.60, D:Y.61, D:H.64 pi-Stacking: D:Y.61 Halogen bonds: D:R.18

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Bromodomain-containing protein 4

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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