SMTL ID : 9e2u.7 (7 other biounits)

Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.11 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x RN9: 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide(Non-covalent)

RN9.1: 19 residues within 4Å: Chain B: F.123, N.372, P.373, H.374, E.398, H.399, S.400, W.401, W.407, W.421, F.423 Chain C: H.97, S.100, H.108, C.109, N.110, Q.111, C.112, G.113 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:F.123, B:W.407, B:W.407, B:W.421, C:H.108 Hydrogen bonds: B:N.372, B:H.399, B:W.401, C:S.100, C:S.100 pi-Stacking: B:H.374

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: C.344, C.347, C.412, C.415 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.344, B:C.347, B:C.412, B:C.415 ZN.3: 4 residues within 4Å: Chain C: C.137, C.140, H.153, H.157 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.137, C:C.140, C:H.153, C:H.157 ZN.4: 4 residues within 4Å: Chain C: C.81, C.84, H.97, H.101 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.81, C:C.84, C:H.97, C:H.101 ZN.5: 5 residues within 4Å: Chain C: C.109, Q.111, C.112, H.125, H.129 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.109, C:C.112, C:H.125, C:H.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Slabicki, M. et al., Expanding the druggable zinc-finger proteome defines properties of drug-induced degradation. Mol.Cell (2025)

Release Date

2025-09-03

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
N

C
R

DNA damage-binding protein 1

Protein cereblon

Zinc finger protein Helios

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