SMTL ID : 7zws.1

Crystal structure of human BCL6 BTB domain in complex with compound 13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 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 15 PLIP interactions: 4 interactions with chain B, 11 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 Water bridges: A:R.12 ALA-TRP-VAL-ILE-PRO-ALA.9: 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 15 PLIP interactions: 11 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, B:R.12

2 x K5I: 2-[3-cyano-6-thiophen-2-yl-4-(trifluoromethyl)pyridin-2-yl]sulfanyl-2-phenyl-ethanoic acid(Non-covalent)

K5I.2: 11 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.57 pi-Stacking: A:Y.57 K5I.10: 11 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 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A pi-Stacking: B:Y.57 Water bridges: A:R.23, A:R.23

8 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: 5 residues within 4Å: Chain A: D.16, L.19, N.20, R.23 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.20, A:R.23 EDO.6: 7 residues within 4Å: Chain A: F.10, D.16, N.20 Chain B: A.51, C.52, H.115 Ligands: EDO.5 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.51, B:H.115, A:N.20 EDO.11: 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.12: 2 residues within 4Å: Chain B: R.97, E.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.98 EDO.13: 5 residues within 4Å: Chain B: D.16, L.19, N.20, R.23 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.20, B:R.23 EDO.14: 7 residues within 4Å: Chain A: A.51, C.52, H.115 Chain B: F.10, D.16, N.20 Ligands: EDO.13 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:H.13, B:D.16, B:N.20, A:A.51, A:H.115

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

DMS.7: 4 residues within 4Å: Chain A: E.40, P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.40 DMS.15: 4 residues within 4Å: Chain B: E.40, P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.40

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

CL.8: 3 residues within 4Å: Chain A: M.113, H.115, V.116 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: M.113, H.115, V.116 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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