SMTL ID : 7zwq.1

Crystal structure of human BCL6 BTB domain in complex with compound 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

4 x K4O: ~{N}-[(2-fluorophenyl)methyl]-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-amine(Non-covalent)

K4O.1: 12 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128 Chain B: N.36, R.39, L.40 Ligands: EDO.15, EDO.18 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:M.66 Water bridges: A:Y.73, B:R.43, B:R.43 pi-Stacking: A:Y.73, A:Y.73 K4O.12: 5 residues within 4Å: Chain A: N.94, M.118, A.119, A.122 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.118 Water bridges: A:N.94, A:A.119 K4O.13: 12 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, Q.128 Ligands: EDO.3, EDO.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.66, A:R.43 pi-Stacking: B:Y.73, B:Y.73 K4O.24: 5 residues within 4Å: Chain B: N.94, M.118, A.119, A.122 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:M.118 Water bridges: B:N.94, B:A.119

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

EDO.2: 2 residues within 4Å: Chain A: Y.16, Q.18 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: H.29, D.32, V.33, N.36 Chain B: A.67, C.68 Ligands: EDO.6, K4O.13 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: D.21, S.22 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: R.41, Q.57, F.58, R.59, L.102 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: D.32, L.35, N.36, R.39 Ligands: EDO.3, K4O.13 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: M.118, M.121, A.122 Ligands: K4O.12 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: S.54, P.91, E.92, I.93, N.94, P.95 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: R.41, D.44, R.59 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: R.43, D.44 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain B: Y.16, Q.18 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: A.67, C.68 Chain B: H.29, D.32, V.33, N.36 Ligands: K4O.1, EDO.18 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain B: D.21, S.22 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: R.41, Q.57, F.58, R.59, L.102 Ligands: EDO.21 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: D.32, L.35, N.36, R.39 Ligands: K4O.1, EDO.15 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: M.118, M.121, A.122 Ligands: K4O.24 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain B: S.54, P.91, E.92, I.93, N.94, P.95 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: R.41, D.44, R.59 Ligands: EDO.17 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: R.43, D.44 Ligand excluded by PLIP

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

DMS.11: 5 residues within 4Å: Chain A: E.56, F.58, P.95, E.96, C.99 No protein-ligand interaction detected (PLIP) DMS.23: 5 residues within 4Å: Chain B: E.56, F.58, P.95, E.96, C.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.56

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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