SMTL ID : 9gao.1

Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x 01: 2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanamide

01.1: 11 residues within 4Å: Chain A: V.253, N.254, P.255, H.281, S.282, W.283, W.289, W.303, F.305 Chain B: P.255, H.256 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.254, A:P.255, A:W.283, A:W.283, A:W.289, A:W.289, A:W.289, A:W.289, A:W.303, A:F.305 Hydrogen bonds: A:H.281, A:H.281, A:W.283 01.3: 10 residues within 4Å: Chain A: P.255 Chain B: N.254, P.255, H.256, H.281, S.282, W.283, W.289, W.303, F.305 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:N.254, B:P.255, B:W.283, B:W.283, B:W.289, B:W.289, B:W.289, B:W.289, B:W.303, B:F.305 Hydrogen bonds: B:H.281, B:W.283

2 x ZN: ZINC ION

ZN.2: 5 residues within 4Å: Chain A: C.226, C.229, T.232, C.294, C.297 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.226, A:C.229, A:C.294, A:C.297 ZN.4: 5 residues within 4Å: Chain B: C.226, C.229, T.232, C.294, C.297 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.226, B:C.229, B:C.294, B:C.297

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

2024-10-02

Peptides

Protein cereblon: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Protein cereblon

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