SMTL ID : 6ton.1

Crystal structure of human BCL6 BTB domain in complex with compound 25b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x NR5: 5-[[5-chloranyl-2-(2,2,6,6-tetramethylmorpholin-4-yl)pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one(Non-covalent)

NR5.1: 14 residues within 4Å: Chain A: M.50, A.51, C.52, G.54, Y.57, Q.112, M.113, E.114, H.115 Chain B: D.16, N.20, R.23, L.24, R.27 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:A.51, A:E.114 Water bridges: A:H.115, A:H.115, A:H.115, B:H.13, B:H.13, B:N.20, B:R.23, B:R.27 NR5.3: 14 residues within 4Å: Chain A: D.16, N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, G.54, Y.57, Q.112, M.113, E.114, H.115 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.57 Hydrogen bonds: B:A.51, B:E.114, B:H.115 Water bridges: B:H.115, B:H.115, A:H.13, A:D.16, A:N.20, A:R.23, A:R.27

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

EDO.2: 4 residues within 4Å: Chain A: E.98, I.101, I.124, S.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.98, A:I.124 EDO.4: 4 residues within 4Å: Chain B: E.98, I.101, I.124, S.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.98, B:I.124 EDO.6: 3 residues within 4Å: Chain A: I.71, N.72 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.72, A:N.72, A:N.72 EDO.8: 3 residues within 4Å: Chain B: I.71, N.72 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.72, B:N.72, B:N.72

2 x ALA- TRP- VAL- ILE- PRO- ALA: ALA-TRP-VAL-ILE-PRO-ALA(Non-covalent)

ALA-TRP-VAL-ILE-PRO-ALA.5: 9 residues within 4Å: Chain A: L.55, I.59, I.71, N.72, L.73, D.74, P.75, Y.110 Ligands: EDO.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.55, A:I.71 Hydrogen bonds: A:N.72, A:N.72, A:D.74, A:D.74 ALA-TRP-VAL-ILE-PRO-ALA.7: 9 residues within 4Å: Chain B: L.55, I.59, I.71, N.72, L.73, D.74, P.75, Y.110 Ligands: EDO.8 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.55, B:I.71 Hydrogen bonds: B:N.72, B:N.72, B:D.74, B:D.74, B:D.74, B:Y.110

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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