SMTL ID : 6too.1

Crystal structure of human BCL6 BTB domain in complex with compound 11a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 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, T.119 Ligands: EDO.5 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10, B:F.88, B:L.94, B:L.94, B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.6: 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, R.12 Ligands: EDO.10 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10, A:F.88, A:L.94, A:L.94, A:T.119 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11, A:T.119 Water bridges: B:T.11

2 x NR8: 2-chloranyl-4-[[1-methyl-3-[(2~{S})-2-oxidanylbutyl]-2-oxidanylidene-benzimidazol-5-yl]amino]pyridine-3-carbonitrile(Non-covalent)

NR8.2: 14 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: D.16, N.20, R.23, L.24, R.27 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:D.16, B:N.20, A:Y.57 Hydrogen bonds: B:N.20, A:M.50, A:E.114 Water bridges: B:N.20, B:R.27 pi-Stacking: A:Y.57 NR8.7: 14 residues within 4Å: Chain A: D.16, N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:D.16, A:N.20, B:Y.57 Hydrogen bonds: A:N.20, B:M.50, B:E.114 Water bridges: A:N.20, A:R.27 pi-Stacking: B:Y.57

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

EDO.3: 2 residues within 4Å: Chain A: D.5, S.6 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: D.28, L.30, T.31, R.43 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.31, A:R.43 Water bridges: A:D.28, A:D.28, A:L.30, A:L.30, A:T.31 EDO.5: 4 residues within 4Å: Chain A: I.8 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) EDO.8: 2 residues within 4Å: Chain B: D.5, S.6 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain B: D.28, L.30, T.31, R.43 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.43 Water bridges: B:D.28, B:L.30, B:L.30, B:T.31 EDO.10: 4 residues within 4Å: Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.6, ALA-TRP-VAL-ILE-PRO-ALA.6, ALA-TRP-VAL-ILE-PRO-ALA.6 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

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