SMTL ID : 7lwg.1

Crystal structure of the BCL6 BTB domain in complex with OICR-12694

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x YN7: 5-{(5S)-1-[2-({3-chloro-6-[(2S)-2,4-dimethylpiperazin-1-yl]-2-fluoropyridin-4-yl}amino)-2-oxoethyl]-4-oxo-4,6,7,8-tetrahydro-1H-dipyrrolo[1,2-a:2',3'-d]pyrimidin-3-yl}-3,4-difluoro-2-hydroxybenzamide(Non-covalent)

YN7.1: 21 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 Ligands: UNX.8 11 PLIP interactions: 6 interactions with chain A, 5 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 pi-Stacking: A:Y.54 Water bridges: B:R.20 pi-Cation interactions: B:R.20 Halogen bonds: B:H.10 YN7.6: 21 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 Ligands: GOL.7 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:H.10, A:N.17, A:R.24, B:M.47, B:E.111, B:H.112, B:V.113 Water bridges: A:D.13, A:R.20 Halogen bonds: A:H.10 pi-Stacking: B:Y.54

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: L.27, D.29, H.42, K.43, T.44 Chain B: L.27, D.29, H.42, K.43, T.44 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:D.29, A:K.43, A:T.44, A:T.44, B:K.43, B:T.44, B:T.44, B:T.44 GOL.7: 4 residues within 4Å: Chain A: D.13 Chain B: E.111, H.112 Ligands: YN7.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.111, B:H.112, A:D.13

4 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 2 residues within 4Å: Chain A: E.37, Q.38 No protein-ligand interaction detected (PLIP) UNX.4: 3 residues within 4Å: Chain A: Q.6, F.7, T.8 No protein-ligand interaction detected (PLIP) UNX.5: 2 residues within 4Å: Chain A: I.56, K.62 No protein-ligand interaction detected (PLIP) UNX.8: 3 residues within 4Å: Chain B: R.20, R.24 Ligands: YN7.1 No protein-ligand interaction detected (PLIP)

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
B

B-cell lymphoma 6 protein

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