SMTL ID : 9oul.1

DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.97 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain B: C.330, Q.332, C.333, C.398, C.401 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.330, B:C.333, B:C.398, B:C.401

1 x 01: N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea

01.2: 15 residues within 4Å: Chain B: L.268, W.271, D.272, S.279, L.280, R.290, C.294, P.296, T.326, L.328, K.341, I.344, S.346, L.349, P.352 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.271, B:W.271, B:L.280, B:P.296, B:T.326, B:L.328, B:I.344 Hydrogen bonds: B:R.290, B:S.346

1 x 02: N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide

02.3: 8 residues within 4Å: Chain B: N.358, P.359, E.384, H.385, W.387, W.393, W.407, F.409 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.387, B:W.393, B:W.393, B:W.407 Hydrogen bonds: B:H.385, B:H.385

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

DNA damage-binding protein 1

Protein cereblon