SMTL ID : 7zww.1

Crystal structure of human BCL6 BTB domain in complex with compound 18

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x K69: 1,3-dimethyl-5-[(6-morpholin-4-ylpyrimidin-4-yl)amino]benzimidazol-2-one(Non-covalent)

K69.1: 13 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130 Chain B: N.36, R.39, L.40, R.43 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.73, A:Y.73 Hydrogen bonds: A:M.66, A:Y.73, A:E.130 Water bridges: A:H.131 K69.4: 13 residues within 4Å: Chain A: N.36, R.39, L.40, R.43 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.73, B:Y.73 Hydrogen bonds: B:M.66, B:Y.73, B:E.130 Water bridges: B:H.131

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: H.29, D.32 Chain B: H.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.29, A:D.32 EDO.3: 4 residues within 4Å: Chain A: E.114, I.117, I.140, S.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.143, A:S.143 Water bridges: A:M.118 EDO.5: 3 residues within 4Å: Chain A: H.131 Chain B: H.29, D.32 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.32, B:D.32 EDO.6: 4 residues within 4Å: Chain B: E.114, I.117, I.140, S.143 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.143, B:S.143 Water bridges: B:M.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pierrat, O.A. et al., Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays. Sci Rep (2022)

Release Date

2022-11-16

Peptides

B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

B-cell lymphoma 6 protein

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