SMTL ID : 8tzx.1 (1 other biounit)

Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.254, C.257, 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.6: 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

1 x U3I: (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione(Non-covalent)

U3I.2: 16 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: T.6, C.7, E.8, V.9, C.10, G.11 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.283, A:W.317, A:W.317, A:W.331 Hydrogen bonds: A:N.282, A:H.309, A:W.311 Salt bridges: A:E.308

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

SO4.3: 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 SO4.5: 4 residues within 4Å: Chain B: H.261, N.262, R.263, Y.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.263 Salt bridges: B:H.261

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

EDO.4: 5 residues within 4Å: Chain B: T.20, N.262, R.263, V.264, Y.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.20, B:N.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ting, P.Y. et al., A molecular glue degrader of the WIZ transcription factor for fetal hemoglobin induction. Science (2024)

Release Date

2024-07-10

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Protein cereblon

DNA damage-binding protein 1

Protein Wiz

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