SMTL ID : 9oty.1

DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.278, C.281, C.346, C.349 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.278, B:C.281, B:C.346, B:C.349

1 x 01: N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide

01.2: 15 residues within 4Å: Chain B: N.306, P.307, H.308, H.333, S.334, W.335, W.341, W.355, F.357 Chain C: V.11, I.26, N.27, T.29, N.30, G.31 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.307, B:W.335, C:V.11, C:I.26, C:I.26 Hydrogen bonds: B:N.306, B:W.335, B:W.355

1 x 02: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea

02.3: 18 residues within 4Å: Chain B: L.216, W.219, D.220, L.223, S.227, L.228, R.238, C.242, L.243, P.244, T.274, K.289, I.292, S.294, L.297, C.298, G.299, P.300 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.219, B:W.219, B:W.219, B:L.228, B:L.243, B:P.244, B:T.274, B:I.292 Hydrogen bonds: B:R.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rizvi, Z. et al., Identification of a cryptic allosteric site on the E3 ligase adapter protein cereblon. To Be Published

Release Date

2025-11-19

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B
Casein kinase I isoform alpha: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Casein kinase I isoform alpha

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