SMTL ID : 7lwe.1

Crystal structure of the BCL6 BTB domain in complex with OICR-7629

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-dimer

Ligands

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

YND.1: 15 residues within 4Å: Chain A: M.51, A.52, C.53, S.54, G.55, Y.58, Q.113, M.114, E.115, H.116 Chain B: N.21, R.24, L.25, R.28 Ligands: ACT.3 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.58 Hydrogen bonds: A:M.51, A:E.115, B:N.21 Water bridges: A:H.116 YND.6: 15 residues within 4Å: Chain A: N.21, R.24, L.25, R.28 Chain B: M.51, A.52, C.53, S.54, G.55, Y.58, Q.113, M.114, E.115, H.116 Ligands: ACT.8 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:N.21, B:M.51, B:E.115 Hydrophobic interactions: B:Y.58 Water bridges: B:H.116

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 5 residues within 4Å: Chain A: F.11, H.14 Chain B: F.89, H.116, V.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.14 FMT.7: 5 residues within 4Å: Chain A: F.89, H.116, V.117 Chain B: F.11, H.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.14 Water bridges: B:D.17, B:D.17

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: G.55, Y.58 Ligands: YND.1 No protein-ligand interaction detected (PLIP) ACT.4: 5 residues within 4Å: Chain A: H.116, T.120, K.123 Chain B: I.9, F.11 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.120 ACT.8: 3 residues within 4Å: Chain B: G.55, Y.58 Ligands: YND.6 No protein-ligand interaction detected (PLIP) ACT.9: 5 residues within 4Å: Chain A: I.9, F.11 Chain B: H.116, T.120, K.123 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.120

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain A: R.67 Chain B: D.29, I.30, L.31 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: D.29, I.30, L.31 Chain B: R.67 Ligand excluded by 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
A

B-cell lymphoma 6 protein

Related Entries With Identical Sequence