SMTL ID : 9oio.2 (3 other biounits)

The von Hippel Lindau-ElonginB-ElonginC (VCB) complex with fragments 9 and 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 02: 1-[6-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-2,3-dihydroindol-1-yl]ethanone

02.1: 8 residues within 4Å: Chain B: E.50, I.51, P.52, V.55, E.88, M.91, A.92, F.95 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.50, B:P.52, B:V.55, B:E.88

1 x 01: 1-[(2-fluorophenyl)methyl]-4-(propan-2-yl)piperazine

01.2: 9 residues within 4Å: Chain C: R.36, W.55, F.58, Y.65, H.77, S.78, Y.79, H.82, W.84 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.58, C:Y.65, C:W.84

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 1 residues within 4Å: Chain C: R.128 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.128, C:S.135 Salt bridges: B:E.78 DMS.4: 6 residues within 4Å: Chain C: R.134, S.135, L.136, V.137, K.138, P.139 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Amporndanai, K. et al., NMR-Based Fragment Screen of the von Hippel-Lindau Elongin C&B Complex. Acs Med.Chem.Lett. (2025)

Release Date

2025-07-09

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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