SMTL ID : 8bdn.3 (3 other biounits)

VCB in complex with compound 23

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.76 Å

Oligo State

hetero-2-1-mer

Ligands

2 x QFR: (2~{R})-3-methyl-1-[(2~{S},4~{R})-2-[(5~{R})-5-methyl-5-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-4~{H}-1,2,4-oxadiazol-3-yl]-4-oxidanyl-pyrrolidin-1-yl]-2-(3-methyl-1,2-oxazol-5-yl)butan-1-one(Non-covalent)

QFR.1: 12 residues within 4Å: Chain A: N.16, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.37, A:Y.47, A:Y.47, A:I.58, A:I.58, A:Y.61, A:W.66 Hydrogen bonds: A:N.16, A:Y.47, A:H.59, A:Y.61, A:H.64 pi-Stacking: A:Y.61 QFR.2: 13 residues within 4Å: Chain C: 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 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:W.37, C:I.58, C:I.58, C:Y.61, C:W.66 Hydrogen bonds: C:Y.47, C:R.56, C:H.59, C:Y.61, C:H.64 pi-Stacking: C:Y.47, 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

von Hippel-Lindau disease tumor suppressor: AC
Elongin-B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

C
L

B
G

von Hippel-Lindau disease tumor suppressor

Elongin-B

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