SMTL ID : 3lbz.1

Crystal Structure of the BCL6 BTB domain complexed with the small molecule inhibitor 79-6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x Z88: N-[(4-bromophenyl)sulfonyl]acetamide(Non-covalent)

Z88.1: 5 residues within 4Å: Chain A: S.5, Q.6, I.7, Q.8 Ligands: Z88.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.7 Hydrogen bonds: A:Q.8 Z88.4: 8 residues within 4Å: Chain A: I.7, Q.8, F.9 Chain B: T.118, K.121, F.122, A.125 Ligands: Z88.1 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.118, B:K.121, B:K.121, A:I.7, A:I.7 Hydrogen bonds: B:T.118

3 x Z89: (2R)-2-[(5Z)-5-(5-bromo-2-oxo-1,2-dihydro-3H-indol-3-ylidene)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]butanedioic acid(Non-covalent)

Z89.2: 9 residues within 4Å: Chain A: N.19, R.22, L.23, R.26 Chain B: M.49, A.50, S.52, G.53, Y.56 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.56, B:Y.56, A:N.19, A:L.23 Hydrogen bonds: B:A.50, A:R.22 Salt bridges: A:R.26 pi-Cation interactions: A:R.22 Z89.3: 9 residues within 4Å: Chain A: M.49, A.50, S.52, G.53, Y.56 Chain B: N.19, R.22, L.23, R.26 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:N.19, B:L.23, A:Y.56 Salt bridges: B:R.26 Hydrogen bonds: A:A.50 pi-Stacking: A:Y.56 Z89.5: 9 residues within 4Å: Chain B: I.58, K.64, L.67, V.69, I.70, N.71, D.73, P.74, Y.109 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:N.71, B:D.73 Hydrogen bonds: B:N.71, B:N.71, B:D.73 Salt bridges: B:K.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cerchietti, L.C. et al., A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo. Cancer Cell (2010)

Release Date

2010-04-28

Peptides

B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

B-cell lymphoma 6 protein

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