SMTL ID : 8p0f.1 (1 other biounit)

Crystal structure of the VCB complex with compound 1.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x WBN: (3~{R},5~{R})-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-5-oxidanyl-2-oxidanylidene-1-pyridin-2-yl-piperidine-3-carboxamide(Non-covalent)

WBN.1: 15 residues within 4Å: Chain A: F.25, P.35, W.37, F.40, Y.47, P.48, T.49, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.37, A:Y.47, A:I.58, A:I.58 Hydrogen bonds: A:H.59, A:S.60, A:Y.61, A:H.64, A:W.66

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: R.56, R.57 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scott, T. et al., Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders. Chemrxiv (2023)

Release Date

2023-05-31

Peptides

von Hippel-Lindau disease tumor suppressor: A
Elongin-C: B
Elongin-B: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

von Hippel-Lindau disease tumor suppressor

Elongin-C

Elongin-B

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