SMTL ID : 9q03.1

Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.15 Å

Oligo State

hetero-2-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain C: C.348, Q.350, C.351, C.416, C.419, S.421 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.348, C:C.351, C:C.416, C:C.419

1 x 01: (3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione

01.2: 29 residues within 4Å: Chain A: M.65, A.66, C.67, G.69, Y.72, F.103, Q.127, M.128, E.129, H.130, V.131 Chain B: H.28, D.31, V.32, N.35, R.38, L.39, R.42 Chain C: V.375, N.376, P.377, H.378, E.402, H.403, S.404, W.405, W.411, W.425, F.427 16 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A, 10 interactions with chain C Hydrogen bonds: B:N.35, A:M.65, A:A.66, A:E.129, C:N.376, C:H.403, C:H.403, C:W.405 Hydrophobic interactions: A:Y.72, C:P.377, C:W.405, C:W.405, C:W.411, C:W.411, C:W.411 pi-Stacking: A:Y.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shunatona, H.P. et al., Discovery of Potent and Selective BCL6 Ligand-Directed Degrader (LDD), BCL6-760. J.Med.Chem. (2025)

Release Date

2025-10-15

Peptides

B-cell lymphoma 6 protein: AB
Protein cereblon: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

B-cell lymphoma 6 protein

Protein cereblon

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