SMTL ID : 8vlb.1

Crystal structure of EloBC-VHL-CDO1 complex bound to compound 4 molecular glue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 3JF: N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide(Non-covalent)

3JF.1: 19 residues within 4Å: Chain A: P.35, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: P.45, W.48, A.49, A.52, F.54, Q.100, P.151 16 PLIP interactions: 6 interactions with chain D, 10 interactions with chain A Hydrophobic interactions: D:P.45, D:A.49, D:A.52, D:F.54, A:Y.47, A:Y.47, A:I.58, A:Y.61, A:W.66 Hydrogen bonds: D:Q.100, D:Q.100, A:W.37, A:R.56, A:H.59, A:Y.61, A:H.64

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 3 residues within 4Å: Chain A: G.53, T.54, G.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.53, A:G.55, A:G.55

1 x FE2: FE (II) ION(Non-covalent)

FE2.3: 3 residues within 4Å: Chain D: H.87, H.89, H.141 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.87, D:H.89, D:H.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tutter, A. et al., A small-molecule VHL molecular glue degrader for cysteine dioxygenase 1. Nat.Chem.Biol. (2025)

Release Date

2024-03-13

Peptides

von Hippel-Lindau disease tumor suppressor: A
Elongin-B: B
Elongin-C: C
Cysteine dioxygenase type 1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

von Hippel-Lindau disease tumor suppressor

Elongin-B

Elongin-C

Cysteine dioxygenase type 1

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