SMTL ID : 5x9p.2 (1 other biounit)

Crystal structure of the BCL6 BTB domain in complex with Compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x 80L: 3-[[4-chloranyl-2-nitro-5-[(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)amino]phenyl]amino]propanoic acid(Non-covalent)

80L.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 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.70, B:Y.70, A:L.37 Hydrogen bonds: B:M.63, B:G.67, B:E.127, A:R.36 Water bridges: B:A.64, B:V.129, A:N.33 80L.2: 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 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.70, A:Y.70, B:L.37 Hydrogen bonds: A:M.63, A:G.67, A:E.127, B:R.36 Water bridges: A:A.64, A:V.129, B:N.33

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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