SMTL ID : 8bb5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

10 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 6 residues within 4Å: Chain A: R.37, F.79, R.80, A.81, T.84, E.86 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.37 SCN.2: 3 residues within 4Å: Chain A: R.9, T.12, L.35 No protein-ligand interaction detected (PLIP) SCN.3: 3 residues within 4Å: Chain C: I.58, H.59 Ligands: Q43.4 No protein-ligand interaction detected (PLIP) SCN.7: 6 residues within 4Å: Chain D: F.253, S.254, V.255, T.256, C.296, H.297 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.255, D:T.256 Water bridges: D:T.256 SCN.8: 4 residues within 4Å: Chain D: N.117, F.136 Ligands: Q43.4, K.6 No protein-ligand interaction detected (PLIP) SCN.9: 4 residues within 4Å: Chain D: N.123, H.165, K.208, F.250 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.123 SCN.10: 6 residues within 4Å: Chain D: S.210, P.211, N.212, Y.215, F.253, L.275 No protein-ligand interaction detected (PLIP) SCN.11: 5 residues within 4Å: Chain D: C.235, L.236, K.237, T.238, K.278 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.238 SCN.12: 5 residues within 4Å: Chain D: T.238, Y.239, T.240, W.273, K.278 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.240 SCN.15: 3 residues within 4Å: Chain D: K.243, E.266, D.267 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.266

1 x Q43: ~{N}-[5-[4-[[4-[2-[[(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]-2-oxidanylidene-ethyl]phenyl]methylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanyl-4-(trifluoromethyl)pyridine-3-carboxamide(Non-covalent)

Q43.4: 33 residues within 4Å: Chain C: N.16, 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: S.36, S.37, A.52, G.76, I.77, S.78, D.79, D.94, F.120, F.136, P.160, S.162, Y.178, C.248, I.292, L.308 Ligands: SCN.3, K.6, SCN.8 25 PLIP interactions: 16 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:W.37, C:F.40, C:I.58, C:I.58, C:W.66, D:F.120, D:F.120, D:F.136, D:P.160, D:Y.178 Hydrogen bonds: C:R.18, C:R.18, C:Y.47, C:R.56, C:H.59, C:S.60, C:Y.61, C:Y.61, C:Y.61, D:S.78 pi-Stacking: C:Y.47, D:F.120 pi-Cation interactions: C:R.18 Water bridges: D:S.78 Salt bridges: D:D.79

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

EDO.5: 4 residues within 4Å: Chain C: N.80, L.84, F.85, V.86 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.80, C:V.86, C:V.86 Water bridges: C:N.80 EDO.13: 5 residues within 4Å: Chain D: C.182, L.196, A.218, T.220, W.228 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.196 Water bridges: D:T.220, D:K.226 EDO.14: 3 residues within 4Å: Chain C: P.20 Chain D: E.138, S.158 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.138 Water bridges: D:S.158, D:S.158 EDO.16: 4 residues within 4Å: Chain D: Y.247, D.289, L.308, E.309 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.289, D:E.309

1 x K: POTASSIUM ION(Non-covalent)

K.6: 3 residues within 4Å: Chain C: Y.61 Ligands: Q43.4, SCN.8 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:Y.61, H2O.7, H2O.8, H2O.11

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
A

B
B

C
C

D
D

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

WD repeat-containing protein 5

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