SMTL ID : 6tol.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

homo-dimer

Ligands

2 x NQW: 5-[[5-chloranyl-2-[(2~{S},6~{R})-2,6-dimethylmorpholin-4-yl]pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one(Non-covalent)

NQW.1: 16 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130, H.131 Chain B: D.32, N.36, R.39, L.40 Ligands: EDO.4, EDO.9 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.73 Hydrogen bonds: A:A.67, A:E.130 Water bridges: A:H.131 pi-Stacking: A:Y.73 NQW.11: 16 residues within 4Å: Chain A: D.32, N.36, R.39, L.40 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130, H.131 Ligands: EDO.14, EDO.19 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.73 Hydrogen bonds: B:A.67, B:E.130 Water bridges: B:Y.73, B:H.131, A:H.29 pi-Stacking: B:Y.73

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

EDO.2: 4 residues within 4Å: Chain A: Y.16, F.17, Q.18, I.24 Ligand excluded by PLIP EDO.3: 1 residues within 4Å: Chain A: Q.57 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: E.130, H.131 Ligands: NQW.1, EDO.9 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: S.54, P.91, E.92, I.93, N.94, P.95 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: E.114, I.117, I.140, S.143 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: L.35, N.38, R.39, S.42 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: T.27, R.28, S.31 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: N.36, R.39 Ligands: NQW.1, EDO.4 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain B: Y.16, F.17, Q.18, I.24 Ligand excluded by PLIP EDO.13: 1 residues within 4Å: Chain B: Q.57 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: E.130, H.131 Ligands: NQW.11, EDO.19 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: S.54, P.91, E.92, I.93, N.94, P.95 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: E.114, I.117, I.140, S.143 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: L.35, N.38, R.39, S.42 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: T.27, R.28, S.31 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: N.36, R.39 Ligands: NQW.11, EDO.14 Ligand excluded by PLIP

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

DMS.10: 1 residues within 4Å: Chain A: C.99 No protein-ligand interaction detected (PLIP) DMS.20: 1 residues within 4Å: Chain B: C.99 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