SMTL ID : 8bb4.1

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with C3 linker

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x Q3R: ~{N}-[5-[4-[[4-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-4-oxidanylidene-butyl]carbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide(Non-covalent)

Q3R.1: 30 residues within 4Å: Chain C: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: S.36, S.37, A.52, G.76, I.77, S.78, D.79, D.94, F.120, F.136, S.162, Y.178, C.248, I.292, L.308 21 PLIP interactions: 12 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:W.37, C:I.58, C:Y.61, C:W.66, D:A.52, D:F.120, D:F.120, D:F.136, D:Y.178, D:Y.178 Hydrogen bonds: C:N.16, C:W.37, C:Y.47, C:R.56, C:H.59, C:Y.61, C:H.64, D:S.78 pi-Stacking: C:Y.47, D:F.120 Salt bridges: D:D.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schwalm, M.P. et al., Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization. Cell Chem Biol (2023)

Release Date

2022-11-09

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
WD repeat-containing protein 5: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
O

C
P

D
Q

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

WD repeat-containing protein 5

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