SMTL ID : 6tok.1

Crystal structure of human BCL6 BTB domain in complex with compound 23d

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 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 Chain B: F.88, R.93, L.94, H.115, T.119 Ligands: DMS.18, EDO.27 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:L.94, A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10 Water bridges: B:T.119, A:R.12 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.19: 12 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 Ligands: EDO.9, DMS.36 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10 Hydrogen bonds: A:T.119, B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11, B:R.12

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

NQT.2: 16 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 Ligands: EDO.7, EDO.14 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:M.50, A:E.114, B:R.27, B:R.27 Water bridges: A:C.52, A:H.115, B:D.16 pi-Cation interactions: B:R.23 NQT.20: 16 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 Ligands: EDO.25, EDO.32 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.57 Hydrogen bonds: B:M.50, B:E.114, A:R.27, A:R.27 Water bridges: B:C.52, B:H.115 pi-Cation interactions: A:R.23

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

EDO.3: 2 residues within 4Å: Chain A: R.97, E.98 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: R.27, D.28, I.29 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: E.98, I.124, S.127 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: E.114, H.115 Ligands: NQT.2 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: S.15, D.16, L.19 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: R.93 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.19, ALA-TRP-VAL-ILE-PRO-ALA.19 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: E.40, Q.41, F.42 Ligands: DMS.15 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.25, S.26, D.28, T.31, R.43 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: R.23 Ligands: EDO.13, DMS.16 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: S.26, R.27 Ligands: EDO.12, DMS.16 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: Y.57 Ligands: NQT.2 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain B: R.97, E.98 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: R.27, D.28, I.29 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: E.98, I.124, S.127 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: E.114, H.115 Ligands: NQT.20 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain B: S.15, D.16, L.19 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: R.93 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: E.40, Q.41, F.42 Ligands: DMS.33 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: R.25, S.26, D.28, T.31, R.43 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: R.23 Ligands: EDO.31, DMS.34 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: S.26, R.27 Ligands: EDO.30, DMS.34 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain B: Y.57 Ligands: NQT.20 Ligand excluded by PLIP

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

DMS.15: 4 residues within 4Å: Chain A: P.79, E.80, C.83 Ligands: EDO.10 No protein-ligand interaction detected (PLIP) DMS.16: 5 residues within 4Å: Chain A: L.19, N.22, S.26 Ligands: EDO.12, EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22 DMS.17: 3 residues within 4Å: Chain A: L.68, S.69, V.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.69, A:V.70 DMS.18: 4 residues within 4Å: Chain B: F.123 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 No protein-ligand interaction detected (PLIP) DMS.33: 4 residues within 4Å: Chain B: P.79, E.80, C.83 Ligands: EDO.28 No protein-ligand interaction detected (PLIP) DMS.34: 5 residues within 4Å: Chain B: L.19, N.22, S.26 Ligands: EDO.30, EDO.31 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.22 DMS.35: 3 residues within 4Å: Chain B: L.68, S.69, V.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.69, B:V.70 DMS.36: 4 residues within 4Å: Chain A: F.123 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.19, ALA-TRP-VAL-ILE-PRO-ALA.19, ALA-TRP-VAL-ILE-PRO-ALA.19 No protein-ligand interaction detected (PLIP)

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

Related Entries With Identical Sequence