SMTL ID : 7ruw.1

Crystal structure of the BCL6 BTB domain in complex with OICR-7859

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

7RR.1: 13 residues within 4Å: Chain A: M.49, A.50, C.51, S.52, G.53, Y.56, Q.111, M.112, E.113, H.114 Chain B: N.19, R.22, L.23 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.56 Hydrogen bonds: A:M.49, A:E.113, B:N.19 Water bridges: A:G.53, A:Q.111, A:H.114 7RR.6: 13 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, Q.111, M.112, E.113, H.114 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.56 Hydrogen bonds: B:M.49, B:E.113, A:N.19 Water bridges: B:G.53, B:Q.111, B:H.114

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

FMT.2: 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.3: 5 residues within 4Å: Chain A: F.9, H.12 Chain B: F.87, H.114, V.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.12 Water bridges: A:D.15, A:D.15 FMT.4: 5 residues within 4Å: Chain A: I.7, Q.8, F.9 Chain B: H.114, T.118 No protein-ligand interaction detected (PLIP) FMT.7: 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.8: 5 residues within 4Å: Chain A: F.87, H.114, V.115 Chain B: F.9, H.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.12 Water bridges: A:H.114 FMT.9: 5 residues within 4Å: Chain A: H.114, T.118 Chain B: I.7, Q.8, F.9 No protein-ligand interaction detected (PLIP)

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

CL.5: 4 residues within 4Å: Chain A: D.27, I.28, L.29 Chain B: R.65 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: R.65 Chain B: D.27, I.28, L.29 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mamai, A. et al., Crystal structure of the BCL6 BTB domain in complex with OICR-7859. 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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