SMTL ID : 7q7t.1

Crystal structure of human BCL6 BTB domain in complex with compound 7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 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: 10 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, R.93, L.94, T.119 Ligands: EDO.9 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10 Water bridges: B:R.93, B:R.93, B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.10: 10 residues within 4Å: Chain A: F.88, R.93, L.94, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 Ligands: EDO.18 15 PLIP interactions: 5 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10 Hydrogen bonds: A:T.119, B:Q.9, B:Q.9, B:T.11 Water bridges: A:R.93, A:R.93, B:T.11

2 x 9FW: 2-chloranyl-4-[[(2S)-2,7-dimethyl-5,6-bis(oxidanylidene)-2,3-dihydro-1H-[1,4]oxazepino[6,5-c]quinolin-10-yl]amino]pyridine-3-carbonitrile(Non-covalent)

9FW.2: 14 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: H.13, D.16, N.20, R.23, L.24 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:D.16 Hydrogen bonds: B:N.20, A:M.50, A:A.51, A:E.114, A:H.115 Water bridges: B:R.27, A:V.116 Salt bridges: A:H.115 pi-Stacking: A:Y.57 9FW.11: 14 residues within 4Å: Chain A: H.13, 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 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:D.16 Hydrogen bonds: A:N.20, B:M.50, B:A.51, B:E.114, B:H.115 Water bridges: A:R.27, B:V.116 Salt bridges: B:H.115 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, I.124 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.98 EDO.6: 2 residues within 4Å: Chain A: Q.41, V.70 No protein-ligand interaction detected (PLIP) EDO.9: 5 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, ALA-TRP-VAL-ILE-PRO-ALA.1 No protein-ligand interaction detected (PLIP) 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, I.124 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.98 EDO.15: 2 residues within 4Å: Chain B: Q.41, V.70 No protein-ligand interaction detected (PLIP) EDO.18: 5 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, ALA-TRP-VAL-ILE-PRO-ALA.10 No protein-ligand interaction detected (PLIP)

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

DMS.7: 2 residues within 4Å: Chain A: E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.16: 2 residues within 4Å: Chain B: E.80, C.83 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: S.69, V.70 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: S.69, V.70 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davis, O.A. et al., Optimizing Shape Complementarity Enables the Discovery of Potent Tricyclic BCL6 Inhibitors. J.Med.Chem. (2022)

Release Date

2022-06-15

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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