SMTL ID : 6toj.1

Crystal structure of human BCL6 BTB domain in complex with compound 17a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x NQQ: 2-chloranyl-4-[[1-methyl-3-(3-methyl-3-oxidanyl-butyl)-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile(Non-covalent)

NQQ.1: 15 residues within 4Å: Chain A: M.66, A.67, C.68, G.70, Y.73, Q.128, M.129, E.130, H.131 Chain B: D.32, N.36, R.39, L.40, R.43 Ligands: EDO.8 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Water bridges: B:H.29, B:R.43, A:H.131, A:H.131 Hydrophobic interactions: A:Y.73, A:Y.73 Hydrogen bonds: A:M.66, A:E.130 NQQ.6: 15 residues within 4Å: Chain A: D.32, N.36, R.39, L.40, R.43 Chain B: M.66, A.67, C.68, G.70, Y.73, Q.128, M.129, E.130, H.131 Ligands: EDO.3 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.73, B:Y.73 Hydrogen bonds: B:M.66, B:E.130 Water bridges: B:E.130, B:H.131, B:H.131, A:R.43

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

EDO.2: 3 residues within 4Å: Chain A: Y.16, F.17, Q.18 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: N.36, R.39 Ligands: NQQ.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.36, A:R.39 Water bridges: A:N.36, A:R.39 EDO.4: 4 residues within 4Å: Chain A: E.56, F.58, E.96, C.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.56 EDO.5: 3 residues within 4Å: Chain A: D.90, I.93, Y.126 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain B: Y.16, F.17, Q.18 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain B: N.36, R.39 Ligands: NQQ.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.36, B:R.39 Water bridges: B:N.36, B:R.39 EDO.9: 4 residues within 4Å: Chain B: E.56, F.58, E.96, C.99 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.56, B:E.56 EDO.10: 3 residues within 4Å: Chain B: D.90, I.93, Y.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.90

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellenie, B.R. et al., AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders. J.Med.Chem. (2020)

Release Date

2020-04-22

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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