SMTL ID : 7zwy.1

Crystal structure of human BCL6 BTB domain in complex with compound 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 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.5: 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: 4 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 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11, B:R.12

2 x K6R: 2-chloranyl-4-[(phenylmethyl)amino]pyridine-3-carbonitrile(Non-covalent)

K6R.2: 7 residues within 4Å: Chain A: M.50, A.51, G.54, Y.57 Chain B: N.20, R.23, L.24 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:N.20, A:Y.57, A:Y.57 Hydrogen bonds: B:R.23, A:M.50 K6R.6: 7 residues within 4Å: Chain A: N.20, R.23, L.24 Chain B: M.50, A.51, G.54, Y.57 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.57, B:Y.57, A:N.20 Hydrogen bonds: B:M.50, A:R.23

2 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.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

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

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