SMTL ID : 5x9o.2 (1 other biounit)

Crystal structure of the BCL6 BTB domain in complex with Compound 1a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 x 80R: 5-[(2-chloranyl-4-nitro-phenyl)amino]-1,3-dihydrobenzimidazol-2-one(Non-covalent)

80R.1: 12 residues within 4Å: Chain A: N.33, R.36, L.37, R.40 Chain B: M.63, A.64, C.65, G.67, Y.70, Q.125, M.126, E.127 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.70, B:Y.70, A:L.37 Hydrogen bonds: B:M.63, B:C.65, B:G.67, B:E.127 80R.4: 12 residues within 4Å: Chain A: M.63, A.64, C.65, G.67, Y.70, Q.125, M.126, E.127 Chain B: N.33, R.36, L.37, R.40 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.70, A:Y.70, B:L.37 Hydrogen bonds: A:M.63, A:C.65, A:G.67, A:E.127

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

EDO.2: 3 residues within 4Å: Chain A: H.26, N.33 Chain B: A.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.26, A:N.33 EDO.5: 3 residues within 4Å: Chain A: A.64 Chain B: H.26, N.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.26, B:N.33

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: S.51, P.88, E.89, I.90 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.88 K.6: 4 residues within 4Å: Chain B: S.51, P.88, E.89, I.90 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:P.88

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yasui, T. et al., Discovery of a novel B-cell lymphoma 6 (BCL6)-corepressor interaction inhibitor by utilizing structure-based drug design. Bioorg. Med. Chem. (2017)

Release Date

2017-08-16

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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