SMTL ID : 8c78.1

Crystal structure of human BCL6 BTB domain in complex with compound CCT374705

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x TWI: (2~{S})-10-[(3-chloranyl-2-fluoranyl-pyridin-4-yl)amino]-2-cyclopropyl-3,3-bis(fluoranyl)-7-methyl-2,4-dihydro-1~{H}-[1,4]oxazepino[2,3-c]quinolin-6-one(Non-covalent)

TWI.1: 17 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, F.104, Q.128, M.129, E.130 Chain B: H.29, D.32, V.33, N.36, R.39, L.40 Ligands: EDO.9 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:D.32, A:Y.73 Water bridges: B:R.43, A:H.131, A:H.131 Hydrogen bonds: A:M.66, A:A.67, A:E.130 pi-Stacking: A:Y.73 TWI.8: 17 residues within 4Å: Chain A: H.29, D.32, V.33, N.36, R.39, L.40 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, F.104, Q.128, M.129, E.130 Ligands: EDO.2 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.73, A:D.32 Hydrogen bonds: B:M.66, B:A.67, B:E.130 Water bridges: B:H.131, B:H.131, A:R.43 pi-Stacking: B:Y.73

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

EDO.2: 3 residues within 4Å: Chain A: N.36, R.39 Ligands: TWI.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:R.39, A:R.39 EDO.3: 1 residues within 4Å: Chain A: A.122 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: R.41, D.44, T.47, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.44, A:R.59 EDO.5: 5 residues within 4Å: Chain A: E.114, I.117, M.118, I.140, S.143 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.143, A:S.143 Water bridges: A:E.114, A:M.118 EDO.9: 3 residues within 4Å: Chain B: N.36, R.39 Ligands: TWI.1 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.36, B:R.39, B:R.39 EDO.10: 1 residues within 4Å: Chain B: A.122 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain B: R.41, D.44, T.47, R.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.44, B:D.44, B:R.59 EDO.12: 5 residues within 4Å: Chain B: E.114, I.117, M.118, I.140, S.143 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.143, B:S.143 Water bridges: B:E.114, B:M.118

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

CL.6: 1 residues within 4Å: Chain A: N.88 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: L.84, S.85, V.86 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: N.88 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: L.84, S.85, V.86 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harnden, A.C. et al., Discovery of an In Vivo Chemical Probe for BCL6 Inhibition by Optimization of Tricyclic Quinolinones. J.Med.Chem. (2023)

Release Date

2023-04-26

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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