SMTL ID : 7u8f.2 (1 other biounit)

Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.286, C.289, C.354, C.357 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.286, A:C.289, A:C.354, A:C.357 ZN.8: 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 LWK: (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione(Non-covalent)

LWK.2: 16 residues within 4Å: Chain A: N.314, P.315, H.316, E.340, H.341, S.342, W.343, W.349, W.363, F.365 Chain C: H.6, C.7, N.8, Q.9, C.10, G.11 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:P.315, A:W.343, A:W.349, A:W.363, C:H.6 Hydrogen bonds: A:N.314, A:H.341, A:H.341, A:W.343 Salt bridges: A:E.340

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: K.364, K.376 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.364, A:K.376 SO4.5: 5 residues within 4Å: Chain B: K.611, E.654, F.703, C.704, H.705 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.705 Salt bridges: B:K.611, B:H.705 SO4.6: 5 residues within 4Å: Chain B: I.220, H.261, N.262, R.263, Y.271 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.262, B:R.263 Salt bridges: B:H.261 SO4.7: 2 residues within 4Å: Chain B: K.560, T.597 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.597, B:T.597, B:T.597 Salt bridges: B:K.560

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 9 residues within 4Å: Chain B: R.270, E.303, L.305, Y.316, G.320, L.336, N.337, V.338, Y.346 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.320 Salt bridges: B:R.270, B:E.303

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bonazzi, S. et al., Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy. Cell Chem Biol (2023)

Release Date

2023-03-08

Peptides

Protein cereblon: A
DNA damage-binding protein 1: B
IKZF2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Protein cereblon

DNA damage-binding protein 1

IKZF2

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