SMTL ID : 7lzs.1

Crystal structure of the BCL6 BTB domain in complex with OICR-11029

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

2 x YJS: 3-chloro-5-{7-[2-({5-chloro-2-[(3S)-3-methylmorpholin-4-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide(Non-covalent)

YJS.1: 19 residues within 4Å: Chain A: F.7, H.10, D.13, V.14, N.17, R.20, L.21 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 7 PLIP interactions: 5 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:N.17 Halogen bonds: A:H.10 YJS.4: 19 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 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.54 Hydrogen bonds: A:M.47, A:E.111, A:H.112, A:V.113, B:N.17 Halogen bonds: B:H.10

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

DMS.2: 8 residues within 4Å: Chain A: I.5, Q.6, F.7, T.8 Chain B: H.112, T.116, K.119 Ligands: SO4.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:K.119 pi-Cation interactions: A:F.7 DMS.5: 8 residues within 4Å: Chain A: H.112, T.116, K.119 Chain B: I.5, Q.6, F.7, T.8 Ligands: SO4.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:K.119 pi-Cation interactions: B:F.7

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: H.112 Chain B: F.7, T.8, R.9, H.10 Ligands: DMS.5 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.8, B:T.8, B:R.9 Water bridges: B:R.9 Salt bridges: B:R.9, A:H.112 SO4.6: 6 residues within 4Å: Chain A: F.7, T.8, R.9, H.10 Chain B: H.112 Ligands: DMS.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.8, A:T.8, A:R.9 Water bridges: A:R.9 Salt bridges: A:R.9, B:H.112

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

2022-03-16

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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