SMTL ID : 8beb.1

Ternary complex between VCB, BRD4-BD1 and PROTAC 49

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.18 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: T.23, F.25, E.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.26

1 x QIK: (2~{S},4~{R})-~{N}-[(1~{S})-3-[4-[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]butylamino]-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)

QIK.2: 20 residues within 4Å: Chain C: W.37, F.40, Y.47, R.57, H.59, S.60, Y.61, H.64, W.66 Chain D: W.40, P.41, F.42, Q.44, L.51, L.53, N.99, D.103, D.104, I.105, M.108 19 PLIP interactions: 9 interactions with chain D, 10 interactions with chain C Hydrophobic interactions: D:W.40, D:P.41, D:F.42, D:L.51, D:L.51, D:L.53, D:I.105, D:I.105, C:W.37, C:Y.47, C:H.59, C:Y.61, C:W.66 Hydrogen bonds: D:N.99, C:Y.47, C:H.59, C:S.60, C:Y.61 pi-Stacking: C:Y.61

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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