SMTL ID : 7lps.1 (3 other biounits)

Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.78 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain B: C.277, C.280, C.345, C.348 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.277, B:C.280, B:C.345, B:C.348 ZN.3: 4 residues within 4Å: Chain C: C.7, C.10, H.23, H.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.7, C:C.10, C:H.23, C:H.27

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)

RN9.2: 17 residues within 4Å: Chain B: F.56, V.304, N.305, P.306, H.307, E.331, H.332, S.333, W.334, W.340, W.354, F.356 Chain C: H.6, C.7, Q.9, C.10, G.11 14 PLIP interactions: 2 interactions with chain C, 12 interactions with chain B Hydrophobic interactions: C:H.6, B:F.56, B:P.306, B:W.340, B:W.340, B:W.340, B:W.354, B:W.354 Hydrogen bonds: C:C.7, B:N.305, B:H.332, B:W.334 pi-Stacking: B:H.307 Halogen bonds: B:P.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, E.S. et al., Acute pharmacological degradation of Helios destabilizes regulatory T cells. Nat.Chem.Biol. (2021)

Release Date

2021-06-02

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

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