SMTL ID : 7zwv.1

Crystal structure of human BCL6 BTB domain in complex with compound 17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 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: 11 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11, R.12 Chain B: F.88, R.93, L.94, H.115, T.119 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10, B:F.88, B:L.94, B:L.94, B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.15: 11 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, R.12 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10, A:F.88, A:L.94, A:L.94, A:T.119 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x KA9: 1,3-dimethyl-5-[[6-(phenylmethylsulfanyl)pyrimidin-4-yl]amino]benzimidazol-2-one(Non-covalent)

KA9.2: 14 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Chain B: N.20, R.23, L.24, R.27 Ligands: GOL.26 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.57, A:Y.57, A:Y.57 Hydrogen bonds: A:M.50, A:E.114 Water bridges: A:Y.57 KA9.16: 14 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, Q.112, M.113, E.114 Ligands: GOL.12 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.57, B:Y.57, B:Y.57 Hydrogen bonds: B:M.50, B:E.114

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

EDO.3: 3 residues within 4Å: Chain A: V.70, I.71, N.72 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: R.27, D.28, I.29 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: E.98, I.101, S.127 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: V.34, Q.41, V.70 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: L.30, T.31, D.32 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: T.31, D.32, V.33, V.34, R.43, S.69 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: D.62, Q.63, L.64 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain B: V.70, I.71, N.72 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: R.27, D.28, I.29 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: E.98, I.101, S.127 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: L.68, S.69, V.70 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: V.34, Q.41, V.70 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: L.30, T.31, D.32 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain B: T.31, D.32, V.33, V.34, R.43, S.69 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: D.62, Q.63, L.64 Ligand excluded by PLIP

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 9 residues within 4Å: Chain A: F.10, H.13, D.16, N.20 Chain B: A.51, C.52, F.88, H.115 Ligands: KA9.16 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.51, A:H.13, A:N.20 Water bridges: B:H.115 GOL.13: 5 residues within 4Å: Chain A: V.36, V.37, S.38, N.72, L.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.38, A:L.73, A:L.73 GOL.26: 9 residues within 4Å: Chain A: A.51, C.52, F.88, H.115 Chain B: F.10, H.13, D.16, N.20 Ligands: KA9.2 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.16, B:N.20, A:A.51 Water bridges: A:H.115 GOL.27: 5 residues within 4Å: Chain B: V.36, V.37, S.38, N.72, L.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.38, B:L.73, B:L.73

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

DMS.14: 3 residues within 4Å: Chain A: P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.28: 3 residues within 4Å: Chain B: P.79, E.80, C.83 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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