SMTL ID : 6tof.1

Crystal structure of human BCL6 BTB domain in complex with compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 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 14 PLIP interactions: 3 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:V.116, 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 Water bridges: A:T.11, A:R.12 ALA-TRP-VAL-ILE-PRO-ALA.7: 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 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:V.116, 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:R.12

2 x NQE: 2-[(1,3-dimethyl-2-oxidanylidene-benzimidazol-5-yl)amino]pyridine-3-carbonitrile(Non-covalent)

NQE.2: 12 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Chain B: N.20, R.23, L.24 7 PLIP interactions: 2 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.20, B:R.23, A:Y.57, A:Y.57, A:Y.57 Hydrogen bonds: A:M.50, A:E.114 NQE.8: 12 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, M.113, E.114 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.57, B:Y.57, B:Y.57, A:N.20, A:R.23 Hydrogen bonds: B:M.50, B:E.114

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

EDO.3: 2 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: D.62, Q.63, L.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:L.64 EDO.5: 4 residues within 4Å: Chain A: R.25, S.26, D.28, R.43 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.26, A:D.28 Water bridges: A:R.43 EDO.6: 2 residues within 4Å: Chain A: M.109, Y.110 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.110 EDO.9: 2 residues within 4Å: Chain B: I.71, N.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.70, B:N.72, B:N.72 EDO.10: 3 residues within 4Å: Chain B: D.62, Q.63, L.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:L.64 EDO.11: 4 residues within 4Å: Chain B: R.25, S.26, D.28, R.43 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.26, B:D.28, B:D.28 Water bridges: B:R.43 EDO.12: 2 residues within 4Å: Chain B: M.109, Y.110 1 PLIP interactions: 1 interactions with chain B Water bridges: 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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