SMTL ID : 7zwp.1

Crystal structure of human BCL6 BTB domain in complex with compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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, V.116, T.119 16 PLIP interactions: 5 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 Water bridges: 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.5: 11 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, V.116, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 16 PLIP interactions: 5 interactions with chain A, 11 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 Water bridges: A:R.93, B:T.11, B:R.12 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11

2 x K4C: ethyl 5-propyl-7-pyridin-4-yl-[1,2,4]triazolo[1,5-a]pyrimidine-6-carboxylate(Non-covalent)

K4C.2: 10 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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.57 Water bridges: A:Y.57 pi-Stacking: A:Y.57 K4C.6: 10 residues within 4Å: Chain A: N.20, R.23, L.24 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.57 pi-Stacking: B:Y.57

4 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: D.62, Q.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:L.64 EDO.7: 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.8: 2 residues within 4Å: Chain B: D.62, Q.63 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:L.64

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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