SMTL ID : 8bb2.1

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

SCN.1: 4 residues within 4Å: Chain A: L.154, P.155, A.156, W.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.156 SCN.2: 4 residues within 4Å: Chain A: L.151, K.152, T.187, A.188 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.152 SCN.5: 4 residues within 4Å: Chain B: R.9, T.12, L.35, F.79 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.9 SCN.9: 4 residues within 4Å: Chain B: F.93 Chain C: H.54, S.57, M.61 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.57 SCN.10: 6 residues within 4Å: Chain D: Q.22, R.57, N.90, G.93, Q.94, P.95 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.57, D:R.57

1 x Q3X: ~{N}-[5-[4-[2-[2-[2-[2-[3-[[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]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide(Non-covalent)

Q3X.3: 33 residues within 4Å: Chain A: A.34, 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, P.203, C.248, I.292, L.308 Chain D: 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 20 PLIP interactions: 11 interactions with chain D, 9 interactions with chain A Hydrophobic interactions: D:W.37, D:I.58, D:Y.61, D:W.66, A:F.120, A:F.120, A:P.160, A:Y.178, A:Y.178 Hydrogen bonds: D:R.56, D:H.59, D:S.60, D:Y.61, D:Y.61, D:H.64, A:S.78 pi-Stacking: D:Y.47, A:F.120 Water bridges: A:S.78 Salt bridges: A:D.79

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

EDO.4: 5 residues within 4Å: Chain A: K.39, N.123, H.165, K.208, F.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.39, A:N.123 Water bridges: A:V.164 EDO.6: 5 residues within 4Å: Chain B: F.25, R.29, P.38, P.39, D.40 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.29, B:R.29, B:D.40, B:D.40 EDO.7: 4 residues within 4Å: Chain B: R.43, F.85, E.86, A.87 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain B: K.46, F.62, A.73, T.74 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.46, B:K.46, B:T.74 Water bridges: B:D.47, B:P.72, B:T.74 EDO.11: 5 residues within 4Å: Chain D: R.31, V.32, D.70, G.72, T.73 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.32, D:G.72 EDO.12: 5 residues within 4Å: Chain C: E.75 Chain D: N.27, R.28, S.29, G.53 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.29, D:S.29, D:G.53 EDO.13: 6 residues within 4Å: Chain D: E.109, L.112, R.116, D.139, H.140, P.141 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.116, D:R.116 Water bridges: D:E.109, D:D.136, D:D.139

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 PEG linker (conformation #2). To Be Published

Release Date

2022-11-09

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
J

C
K

D
L

WD repeat-containing protein 5

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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