SMTL ID : 8bb5.1

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

Coordinates

PDB Format

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: 9 interactions with chain D, 16 interactions with chain C Hydrophobic interactions: D:F.120, D:F.120, D:F.136, D:P.160, D:Y.178, C:W.37, C:F.40, C:I.58, C:I.58, C:W.66 Hydrogen bonds: D:S.78, 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 Water bridges: D:S.78 Salt bridges: D:D.79 pi-Stacking: D:F.120, C:Y.47 pi-Cation interactions: C:R.18

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

Kraemer, A. et al., Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with Aryl linker. To Be Published

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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