SMTL ID : 9djx.2 (1 other biounit)

Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.254, C.257, T.260, C.322, C.325 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.254, A:C.257, A:C.322, A:C.325 ZN.5: 4 residues within 4Å: Chain C: C.7, C.10, H.23, H.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.7, C:C.10, C:H.23, C:H.27

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.187, Q.191, N.247 Chain B: A.537 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.191, A:N.247 Salt bridges: A:R.187 SO4.4: 5 residues within 4Å: Chain B: K.560, Y.587, L.595, R.596, T.597 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.597 Salt bridges: B:K.560

1 x 01: (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione

01.3: 17 residues within 4Å: Chain A: N.282, P.283, H.284, E.308, H.309, S.310, W.311, W.317, W.331, F.333 Chain C: S.3, T.6, C.7, E.8, V.9, C.10, G.11 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.283, A:W.317, A:W.317, A:F.333, C:T.6 Hydrogen bonds: A:N.282, A:H.309, A:W.311 Salt bridges: A:E.308

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kerrigan, J.R. et al., Discovery and Optimization of First-in-Class Molecular Glue Degraders of the WIZ Transcription Factor for Fetal Hemoglobin Induction to Treat Sickle Cell Disease. J.Med.Chem. (2024)

Release Date

2024-11-27

Peptides

Protein cereblon: A
DNA damage-binding protein 1: B
Protein Wiz: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Protein cereblon

DNA damage-binding protein 1

Protein Wiz

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