SMTL ID : 7zwx.1

Crystal structure of human BCL6 BTB domain in complex with compound 19

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 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: 12 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, V.116, T.119 15 PLIP interactions: 11 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 Water bridges: A:R.12 ALA-TRP-VAL-ILE-PRO-ALA.9: 12 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, R.12 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 KA0: 6-[1,3-benzodioxol-5-ylmethyl(methyl)amino]-1-~{tert}-butyl-5~{H}-pyrazolo[3,4-d]pyrimidin-4-one(Non-covalent)

KA0.2: 11 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, S.58, Q.112 Chain B: N.20, R.23, L.24 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:M.50, A:Q.112 KA0.10: 11 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, S.58, Q.112 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.57 Hydrogen bonds: B:M.50, B:Q.112, A:R.27

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: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: E.98, I.101 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.98 Water bridges: A:M.102, A:I.124 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: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 No protein-ligand interaction detected (PLIP) EDO.14: 2 residues within 4Å: Chain B: E.98, I.101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.98 Water bridges: B:M.102, B:I.124

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

CL.7: 3 residues within 4Å: Chain A: M.113, H.115, V.116 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: M.113, H.115, V.116 Ligand excluded by PLIP

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

DMS.8: 5 residues within 4Å: Chain A: E.40, F.42, P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.40 DMS.16: 5 residues within 4Å: Chain B: E.40, F.42, P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.40

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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