SMTL ID : 7zwr.1

Crystal structure of human BCL6 BTB domain in complex with compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

2 x ALA- TRP- VAL- ILE- PRO- ALA: ALA-TRP-VAL-ILE-PRO-ALA(Non-covalent)

ALA-TRP-VAL-ILE-PRO-ALA.1: 10 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, R.93, L.94, H.115, T.119 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:L.94, B:T.119, A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.11: 10 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, A:T.119, B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x K4X: 2-[2-[[(6~{S})-3-cyano-6-methyl-4-(trifluoromethyl)-5,6,7,8-tetrahydroquinolin-2-yl]sulfanyl]ethanoylamino]ethanoic acid(Non-covalent)

K4X.2: 10 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57 Chain B: N.20, R.23, L.24, R.27 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:R.27, A:Y.57 Water bridges: B:R.23, B:R.23, B:R.23 pi-Cation interactions: B:R.23 Hydrophobic interactions: A:Y.57 pi-Stacking: A:Y.57 Halogen bonds: A:M.50 K4X.12: 10 residues within 4Å: Chain A: N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.57 pi-Stacking: B:Y.57 Halogen bonds: B:M.50 Hydrogen bonds: A:R.27 Water bridges: A:R.23, A:R.23, A:R.23 pi-Cation interactions: A:R.23

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

EDO.3: 3 residues within 4Å: Chain A: D.62, Q.63, L.64 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: V.70, I.71, N.72 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: D.28, T.31, R.43 Ligands: EDO.6 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: L.30, T.31, D.32 Ligands: EDO.5 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: V.36, S.38, N.72, L.73, P.75 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: P.79, E.80, C.83 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: E.98, I.101 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain B: D.62, Q.63, L.64 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: V.70, I.71, N.72 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: D.28, T.31, R.43 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: L.30, T.31, D.32 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: V.36, S.38, N.72, L.73, P.75 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: L.68, S.69, V.70 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: P.79, E.80, C.83 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: E.98, I.101 Ligand excluded by 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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