SMTL ID : 9q22.1

Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.41 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x 01: (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione

01.1: 16 residues within 4Å: Chain B: N.335, P.336, H.337, E.361, H.362, S.363, W.364, W.370, W.384, F.386 Chain C: H.9, C.10, N.11, Q.12, C.13, G.14 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.336, B:W.364, B:W.370, B:W.370, B:W.384, B:F.386, C:H.9 Hydrogen bonds: B:N.335, B:H.337, B:H.362, B:H.362, B:W.364 Salt bridges: B:E.361

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain B: C.307, Q.309, C.310, T.313, C.375, I.377, C.378 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.307, B:C.310, B:C.375, B:C.378 ZN.3: 7 residues within 4Å: Chain C: C.10, Q.12, C.13, G.14, A.15, H.26, H.30 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.10, C:C.13, C:H.26, C:H.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luchini, G. et al., Application of Weighted Interaction-Fingerprints for Rationalizing Neosubstrate Potency and Selectivity of Cereblon-Based Molecular Glues. J.Med.Chem. (2025)

Release Date

2025-10-01

Peptides

DNA damage-binding protein 1: A
Protein cereblon: B
Zinc finger protein Helios: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DNA damage-binding protein 1

Protein cereblon

Zinc finger protein Helios

Related Entries With Identical Sequence