SMTL ID : 7zwt.1

Crystal structure of human BCL6 BTB domain in complex with compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x K5U: 2-[(2-chlorophenyl)amino]-~{N}-(pyridin-2-ylmethyl)-1,3-thiazole-4-carboxamide(Non-covalent)

K5U.1: 9 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73 Chain B: N.36, R.39, L.40 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.73 Hydrogen bonds: A:M.66, A:Y.73 pi-Stacking: A:Y.73 Halogen bonds: A:A.67 Water bridges: B:N.36 K5U.6: 9 residues within 4Å: Chain A: N.36, R.39, L.40 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.73 Hydrogen bonds: B:M.66 pi-Stacking: B:Y.73 Halogen bonds: B:A.67 Water bridges: A:N.36

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 2 residues within 4Å: Chain A: Y.16, Q.18 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: Y.16, Q.18 Ligand excluded by PLIP

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

EDO.3: 2 residues within 4Å: Chain A: P.91, E.92 No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: M.118, A.122 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.118 EDO.8: 2 residues within 4Å: Chain B: P.91, E.92 No protein-ligand interaction detected (PLIP) EDO.9: 2 residues within 4Å: Chain B: M.118, A.122 1 PLIP interactions: 1 interactions with chain B Water bridges: B:M.118

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 2 residues within 4Å: Chain A: E.96, C.99 No protein-ligand interaction detected (PLIP) DMS.10: 2 residues within 4Å: Chain B: E.96, C.99 No protein-ligand interaction detected (PLIP)

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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