SMTL ID : 7q7v.1

Crystal structure of human BCL6 BTB domain in complex with compound 12a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

2 x 9GR: 2-chloranyl-4-[[(2R)-2-cyclopropyl-7-methyl-6-oxidanylidene-1,2,3,4-tetrahydro-[1,4]oxazepino[2,3-c]quinolin-10-yl]amino]pyridine-3-carbonitrile(Non-covalent)

9GR.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 Chain B: H.29, D.32, V.33, N.36, R.39, L.40, R.43 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.66, A:A.67, A:E.130 Water bridges: A:H.131, A:H.131, A:H.131, B:N.36, B:R.43 pi-Stacking: A:Y.73 Hydrophobic interactions: B:D.32 9GR.5: 16 residues within 4Å: Chain A: H.29, D.32, V.33, N.36, R.39, L.40, R.43 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.66, B:A.67, B:E.130 Water bridges: B:H.131, B:H.131, B:H.131, A:N.36, A:R.43 pi-Stacking: B:Y.73 Hydrophobic interactions: A:D.32

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

EDO.2: 5 residues within 4Å: Chain A: Y.16, F.17, Q.18, I.24 Chain B: F.139 No protein-ligand interaction detected (PLIP) EDO.3: 3 residues within 4Å: Chain A: E.114, I.117, I.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.114 EDO.6: 5 residues within 4Å: Chain A: F.139 Chain B: Y.16, F.17, Q.18, I.24 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain B: E.114, I.117, I.140 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.114

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

DMS.4: 3 residues within 4Å: Chain A: E.56, F.58, E.96 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.56 DMS.8: 3 residues within 4Å: Chain B: E.56, F.58, E.96 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.56

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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