SMTL ID : 9bju.4 (3 other biounits)

Crystal structure of the complex between VHL, ElonginB, ElonginC, and compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ACE- TBG- HYP- 01- NH2: 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE(Non-covalent)

ACE-TBG-HYP-01-NH2.1: 14 residues within 4Å: Chain C: F.39, P.49, W.51, F.54, Y.61, P.62, R.70, I.72, H.73, S.74, Y.75, H.78, W.80 Ligands: DMS.4 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.39, C:P.49, C:W.51, C:F.54, C:Y.61, C:P.62, C:I.72, C:Y.75, C:W.80 Hydrogen bonds: C:H.73, C:S.74, C:Y.75, C:H.78 pi-Stacking: C:Y.61

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

EDO.2: 5 residues within 4Å: Chain B: E.48, I.49, E.86, M.89, A.90 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.48, B:E.86

1 x TFA: trifluoroacetic acid(Non-covalent)

TFA.3: 4 residues within 4Å: Chain B: Y.2, V.3, K.4, I.14 No protein-ligand interaction detected (PLIP)

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

DMS.4: 5 residues within 4Å: Chain C: R.70, R.71, I.72, H.73 Ligands: ACE-TBG-HYP-01-NH2.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H. et al., Potency-enhanced peptidomimetic VHL ligands with improved oral bioavailability. To Be Published

Release Date

2024-05-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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