SMTL ID : 8bdt.2 (1 other biounit)

Ternary complex between VCB, BRD4-BD2 and PROTAC 51

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 4 residues within 4Å: Chain C: S.71, S.72, T.73, E.74 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.72, C:T.73, C:E.74, C:E.74

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

QLX.2: 25 residues within 4Å: Chain A: P.44, F.45, A.53, L.54, G.55, L.56, C.98, Y.101, 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 23 PLIP interactions: 8 interactions with chain A, 15 interactions with chain D Hydrophobic interactions: A:P.44, A:F.45, A:L.54, A:Y.101, A:V.108, A:V.108, D:Y.47, D:P.48, D:I.58, D:H.59, D:Y.61, D:W.66 Hydrogen bonds: A:N.102, A:N.102, D:Y.47, D:H.59, D:H.59, D:S.60, D:Y.61, D:H.64 pi-Stacking: D:Y.47, 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
E

B
F

C
G

D
H

Bromodomain-containing protein 4

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

Related Entries With Identical Sequence