SMTL ID : 7lwf.1

Crystal structure of the BCL6 BTB domain in complex with OICR-9320

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-dimer

Ligands

2 x YNA: N-(3-chloropyridin-4-yl)-2-[5-(3-cyano-4-hydroxyphenyl)-3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]acetamide(Non-covalent)

YNA.1: 20 residues within 4Å: Chain A: F.7, H.10, D.13, V.14, N.17, R.20, L.21, R.24 Chain B: M.47, A.48, C.49, S.50, G.51, Y.54, F.85, Q.109, M.110, E.111, H.112, V.113 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.54 Hydrogen bonds: B:M.47, B:E.111, B:H.112, B:V.113, A:H.10, A:N.17 Water bridges: B:H.112 YNA.3: 20 residues within 4Å: Chain A: M.47, A.48, C.49, S.50, G.51, Y.54, F.85, Q.109, M.110, E.111, H.112, V.113 Chain B: F.7, H.10, D.13, V.14, N.17, R.20, L.21, R.24 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.54 Hydrogen bonds: A:M.47, A:E.111, A:H.112, A:V.113, B:H.10, B:N.17 Water bridges: B:D.13

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: L.27, T.28, D.29, H.42, K.43, T.44 Chain B: L.27, D.29, H.42, K.43, T.44 Ligands: GOL.4 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.29, A:K.43, A:T.44, A:T.44, B:T.44, B:T.44 GOL.4: 12 residues within 4Å: Chain A: L.27, D.29, H.42, K.43, T.44 Chain B: L.27, T.28, D.29, H.42, K.43, T.44 Ligands: GOL.2 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.44, A:T.44, B:D.29, B:K.43, B:T.44, B:T.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mamai, A. et al., Discovery of OICR12694: A Novel, Potent, Selective, and Orally Bioavailable BCL6 BTB Inhibitor. Acs Med.Chem.Lett. (2023)

Release Date

2022-03-09

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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