SMTL ID : 8rqc.1

Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

4 x ZN: ZINC ION

ZN.1: 6 residues within 4Å: Chain A: C.226, C.229, T.232, C.294, C.297, S.299 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.226, A:C.229, A:C.294, A:C.297 ZN.3: 4 residues within 4Å: Chain B: C.9, C.12, H.25, H.29 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.9, B:C.12, B:H.25, B:H.29 ZN.4: 5 residues within 4Å: Chain C: C.226, C.229, T.232, C.294, C.297 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.226, C:C.229, C:C.294, C:C.297 ZN.6: 4 residues within 4Å: Chain D: C.9, C.12, H.25, H.29 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.9, D:C.12, D:H.25, D:H.29

2 x QFC: Mezigdomide

QFC.2: 18 residues within 4Å: Chain A: F.63, D.110, N.254, P.255, H.256, E.280, H.281, S.282, W.283, W.289, W.303, F.305 Chain B: Q.8, C.9, N.10, Q.11, C.12, G.13 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:Q.8, A:P.255, A:W.283, A:W.289, A:W.289, A:W.289, A:W.303, A:F.305 Hydrogen bonds: B:Q.8, A:N.254, A:E.280, A:H.281, A:H.281, A:W.283 pi-Stacking: A:F.63 QFC.5: 22 residues within 4Å: Chain A: K.220 Chain C: F.63, D.110, F.111, I.113, I.115, N.254, P.255, H.256, E.280, H.281, S.282, W.283, W.289, W.303, F.305 Chain D: Q.8, C.9, N.10, Q.11, C.12, G.13 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.63, C:I.113, C:P.255, C:P.255, C:W.283, C:W.289, C:W.303, D:Q.8 Hydrogen bonds: C:N.254, C:W.283, C:W.283, D:Q.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kroupova, A. et al., Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders. Nat Commun (2024)

Release Date

2024-09-25

Peptides

Protein cereblon: AC
DNA-binding protein Ikaros: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

Protein cereblon

DNA-binding protein Ikaros

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