SMTL ID : 6toi.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 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: 11 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: EDO.9 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:L.94, B:T.119, 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, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.10: 11 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.18 13 PLIP interactions: 4 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, A:T.119, 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:T.11

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

NQN.2: 13 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 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.57, B:D.16, B:N.20 Hydrogen bonds: A:M.50, A:E.114 Water bridges: A:H.115, A:H.115, A:H.115, B:D.16, B:R.27 pi-Stacking: A:Y.57 NQN.11: 13 residues within 4Å: Chain A: D.16, N.20, R.23, L.24 Chain B: M.50, A.51, C.52, G.54, Y.57, Q.112, M.113, E.114, H.115 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:D.16, A:N.20, B:Y.57 Water bridges: A:H.13, A:R.27, B:E.114, B:H.115, B:H.115, B:H.115 Hydrogen bonds: B:M.50, B:E.114 pi-Stacking: B:Y.57

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

EDO.3: 2 residues within 4Å: Chain A: R.97, E.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.98 Water bridges: A:R.97, A:G.99 EDO.4: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.110 EDO.5: 3 residues within 4Å: Chain A: E.98, I.101, S.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.127, A:S.127 Water bridges: A:M.102 EDO.6: 2 residues within 4Å: Chain A: P.75, E.76 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: I.8 Chain B: F.123 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.119 EDO.12: 2 residues within 4Å: Chain B: R.97, E.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.98 Water bridges: B:R.97, B:G.99 EDO.13: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.110 EDO.14: 3 residues within 4Å: Chain B: E.98, I.101, S.127 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.127, B:S.127 Water bridges: B:M.102 EDO.15: 2 residues within 4Å: Chain B: P.75, E.76 No protein-ligand interaction detected (PLIP) EDO.18: 4 residues within 4Å: Chain A: F.123 Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.10, ALA-TRP-VAL-ILE-PRO-ALA.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.119

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

DMS.7: 4 residues within 4Å: Chain A: V.34, V.36, Q.41, V.70 No protein-ligand interaction detected (PLIP) DMS.8: 3 residues within 4Å: Chain A: P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.16: 4 residues within 4Å: Chain B: V.34, V.36, Q.41, V.70 No protein-ligand interaction detected (PLIP) DMS.17: 3 residues within 4Å: Chain B: P.79, E.80, C.83 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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