SMTL ID : 9bol.1 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Q.70 Chain B: P.75, E.76, P.78 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.76, B:E.76, A:Q.70 EDO.2: 4 residues within 4Å: Chain A: I.34 Chain B: Y.2, V.3, I.14 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.34 EDO.3: 3 residues within 4Å: Chain C: P.60, Y.61, P.62 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.60

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

DMS.4: 5 residues within 4Å: Chain C: V.50, P.58, P.60, H.88, V.157 No protein-ligand interaction detected (PLIP)

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

CL.5: 1 residues within 4Å: Chain C: R.124 Ligand excluded by PLIP

1 x 01: (4R)-1-[(2S)-2-(4-cyclopropyl-1H-1,2,3-triazol-1-yl)-3,3-dimethylbutanoyl]-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide

01.6: 15 residues within 4Å: Chain C: R.32, F.39, P.49, W.51, F.54, Y.61, P.62, L.64, R.70, I.72, H.73, S.74, Y.75, H.78, W.80 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:R.32, C:R.32, C:W.51, C:W.51, C:Y.61, C:Y.61, C:I.72, C:I.72, C:Y.75, C:W.80 Hydrogen bonds: C:Y.61, C:R.70, C:H.73, C:S.74, C:Y.75 pi-Stacking: C:Y.75

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
A

B
B

C
C

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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