SMTL ID : 8cql.1

pVHL:EloB:EloC in complex with (2S,4R)-N-((S)-1-(5-Fluoro-2-methoxy-4-(4-methylthiazol-5-yl)phenyl)ethyl)-1-((S)-2-(1-fluorocyclopropane-1-carboxamido)-3,3-dimethylbutanoyl)-4-hydroxypyrrolidine-2-carboxamide (Compound 33)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

hetero-4-4-4-mer

Ligands

4 x VH3: (2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-[5-fluoranyl-2-methoxy-4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide(Non-covalent)

VH3.1: 16 residues within 4Å: Chain C: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, 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:R.18, C:W.37, C:W.37, C:I.58, C:Y.61, C:W.66 Hydrogen bonds: C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64 pi-Stacking: C:Y.47 VH3.2: 16 residues within 4Å: Chain F: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:R.18, F:W.37, F:I.58, F:Y.61, F:W.66 Hydrogen bonds: F:R.56, F:H.59, F:Y.61, F:H.64, F:W.66 pi-Stacking: F:Y.47 VH3.3: 16 residues within 4Å: Chain I: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 11 PLIP interactions: 11 interactions with chain I Hydrophobic interactions: I:W.37, I:Y.61, I:W.66 Hydrogen bonds: I:Y.47, I:R.56, I:H.59, I:S.60, I:Y.61 Water bridges: I:Y.61, I:Y.61 pi-Stacking: I:Y.47 VH3.4: 16 residues within 4Å: Chain L: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, L.50, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 12 PLIP interactions: 12 interactions with chain L Hydrophobic interactions: L:R.18, L:W.37, L:Y.47, L:I.58, L:Y.61, L:W.66 Hydrogen bonds: L:R.56, L:H.59, L:S.60, L:Y.61, L:H.64 pi-Stacking: L:Y.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vu, L.P. et al., Expanding the Structural Diversity at the Phenylene Core of Ligands for the von Hippel-Lindau E3 Ubiquitin Ligase: Development of Highly Potent Hypoxia-Inducible Factor-1 alpha Stabilizers. J.Med.Chem. (2023)

Release Date

2023-09-27

Peptides

Elongin-B: ADGJ
Elongin-C: BEHK
von Hippel-Lindau disease tumor suppressor: CFIL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

G
G

J
J

B
B

E
E

H
H

K
K

C
C

F
F

I
I

L
L

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

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