SMTL ID : 7ruz.1

Crystal structure of the BCL6 BTB domain in complex with OICR-8445

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-dimer

Ligands

2 x 7S5: 2-[2-(benzylamino)-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl]-N-(3-chloropyridin-4-yl)acetamide(Non-covalent)

7S5.1: 15 residues within 4Å: Chain A: M.49, A.50, C.51, S.52, G.53, Y.56, S.57, Q.111, M.112, E.113, H.114 Chain B: N.19, R.22, L.23 Ligands: FMT.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.56, A:Y.56, A:Y.56 Hydrogen bonds: A:M.49, A:E.113, B:N.19 Water bridges: A:H.114 7S5.7: 15 residues within 4Å: Chain A: N.19, R.22, L.23 Chain B: M.49, A.50, C.51, S.52, G.53, Y.56, S.57, Q.111, M.112, E.113, H.114 Ligands: FMT.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.56, B:Y.56, B:Y.56 Hydrogen bonds: B:M.49, B:E.113, A:N.19 Water bridges: B:H.114

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

FMT.2: 6 residues within 4Å: Chain A: I.7, Q.8, F.9 Chain B: H.114, T.118, K.121 No protein-ligand interaction detected (PLIP) FMT.3: 5 residues within 4Å: Chain A: E.39, F.41, P.78, E.79, N.82 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.82 FMT.4: 7 residues within 4Å: Chain A: A.50, C.51 Chain B: H.12, D.15, N.19 Ligands: 7S5.1, FMT.11 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:N.19 Hydrogen bonds: A:A.50 FMT.5: 6 residues within 4Å: Chain A: F.9, H.12 Chain B: F.87, H.114, V.115 Ligands: FMT.10 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.15, B:H.114 FMT.8: 6 residues within 4Å: Chain A: H.114, T.118, K.121 Chain B: I.7, Q.8, F.9 No protein-ligand interaction detected (PLIP) FMT.9: 5 residues within 4Å: Chain B: E.39, F.41, P.78, E.79, N.82 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.82 FMT.10: 7 residues within 4Å: Chain A: H.12, D.15, N.19 Chain B: A.50, C.51 Ligands: FMT.5, 7S5.7 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:N.19 Hydrogen bonds: B:A.50 FMT.11: 6 residues within 4Å: Chain A: F.87, H.114, V.115 Chain B: F.9, H.12 Ligands: FMT.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.114

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

CL.6: 4 residues within 4Å: Chain A: R.65 Chain B: D.27, I.28, L.29 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: D.27, I.28, L.29 Chain B: R.65 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Watson, I. et al., Crystal structure of the BCL6 BTB domain in complex with OICR-8445. To Be Published

Release Date

2022-11-09

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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