SMTL ID : 8d80.1

Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.323, C.326, C.391, C.394 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.323, B:C.326, B:C.391, B:C.394 ZN.3: 5 residues within 4Å: Chain C: C.38, Q.40, C.41, H.54, H.58 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.38, C:H.54, C:H.58

1 x 8W7: (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione(Non-covalent)

8W7.2: 13 residues within 4Å: Chain B: N.351, P.352, H.353, H.357, H.378, S.379, W.380, W.386, W.400, F.402 Chain C: Q.37, C.41, G.42 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:N.351, B:P.352, B:P.352, B:W.380, B:W.386, B:W.386, B:W.400 Hydrogen bonds: B:W.380, B:W.380

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, E.R. et al., Molecular glue CELMoD compounds are regulators of cereblon conformation. Science (2022)

Release Date

2022-07-20

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

DNA-binding protein Ikaros

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