SMTL ID : 8vl9.1

Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x 01: N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen-1-yl]methyl}-L-prolinamide

01.1: 23 residues within 4Å: Chain A: 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 Chain B: P.45, W.48, A.49, A.52, F.54, D.55, Q.56, G.79, Q.100, P.151 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:W.37, A:Y.47, A:Y.47, A:Y.47, A:P.48, A:I.58, A:I.58, A:Y.61, A:W.66, B:P.45, B:P.45, B:A.49, B:F.54, B:F.54 Hydrogen bonds: A:R.56, A:H.59, A:S.60, A:Y.61, A:Y.61, A:H.64, B:Q.56, B:Q.100, B:Q.100

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

CIT.2: 3 residues within 4Å: Chain A: G.53, T.54, G.55 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.53, A:G.55, A:G.55, A:G.55 Water bridges: A:G.55, A:G.55

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

FE2.3: 4 residues within 4Å: Chain B: H.87, H.89, H.141, Y.158 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.87, B:H.89, B: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. To Be Published

Release Date

2024-03-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
B

D
C

von Hippel-Lindau disease tumor suppressor

Cysteine dioxygenase type 1

Elongin-B

Elongin-C

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