SMTL ID : 7zwu.1

Crystal structure of human BCL6 BTB domain in complex with compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 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 Chain B: F.88, R.93, L.94, H.115, T.119 Ligands: EDO.8 16 PLIP interactions: 6 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:Q.9, A:F.10, A:F.10, A:F.10 Water bridges: B:R.93, B:R.93, A:R.12 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.13: 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 Ligands: EDO.20 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: 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, B:R.12, A:R.93, A:R.93

2 x K8R: ~{N}-(3-morpholin-4-ylpropyl)-2-(naphthalen-1-ylamino)-1,3-thiazole-4-carboxamide(Non-covalent)

K8R.2: 13 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112 Chain B: N.20, R.23, L.24, R.27 Ligands: EDO.5, DMS.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:M.50 pi-Stacking: A:Y.57 K8R.14: 13 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 Ligands: EDO.17, DMS.24 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.57 Hydrogen bonds: B:M.50, A:R.27 pi-Stacking: B:Y.57

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

EDO.3: 3 residues within 4Å: Chain A: V.70, I.71, N.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.70, A:N.72, A:N.72 EDO.4: 2 residues within 4Å: Chain A: R.97, E.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.98 EDO.5: 3 residues within 4Å: Chain B: N.20, R.23 Ligands: K8R.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.20 Water bridges: B:R.23, B:R.23 EDO.6: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.74 Water bridges: A:Y.110 EDO.7: 2 residues within 4Å: Chain A: E.98, I.101 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.102 EDO.8: 5 residues within 4Å: Chain A: D.5, S.6, C.7 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.7 EDO.9: 3 residues within 4Å: Chain A: L.68, S.69, V.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.69 EDO.15: 3 residues within 4Å: Chain B: V.70, I.71, N.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.70, B:N.72, B:N.72 EDO.16: 2 residues within 4Å: Chain B: R.97, E.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.98 EDO.17: 3 residues within 4Å: Chain A: N.20, R.23 Ligands: K8R.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20 Water bridges: A:R.23, A:R.23 EDO.18: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.74 Water bridges: B:Y.110 EDO.19: 2 residues within 4Å: Chain B: E.98, I.101 1 PLIP interactions: 1 interactions with chain B Water bridges: B:M.102 EDO.20: 5 residues within 4Å: Chain B: D.5, S.6, C.7 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.13, ALA-TRP-VAL-ILE-PRO-ALA.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.7 EDO.21: 3 residues within 4Å: Chain B: L.68, S.69, V.70 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.69

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

CL.10: 3 residues within 4Å: Chain A: M.113, H.115, V.116 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: M.113, H.115, V.116 Ligand excluded by PLIP

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

DMS.11: 4 residues within 4Å: Chain A: E.40, P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.12: 4 residues within 4Å: Chain A: G.54, S.58, Q.112 Ligands: K8R.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.58 Water bridges: A:Q.112 DMS.23: 4 residues within 4Å: Chain B: E.40, P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.24: 4 residues within 4Å: Chain B: G.54, S.58, Q.112 Ligands: K8R.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.58 Water bridges: B:Q.112

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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