SMTL ID : 7ruy.1

Crystal structure of the BCL6 BTB domain in complex with OICR-8388

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-dimer

Ligands

2 x 7S0: N-(3-chloropyridin-4-yl)-2-(2-{[(2,4-dimethoxyphenyl)methyl]amino}-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide(Non-covalent)

7S0.1: 15 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 Ligands: FMT.3, FMT.10 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.56, A:Y.56 Hydrogen bonds: A:M.49, A:Y.56, A:E.113, B:N.19 Water bridges: A:Q.111, A:H.114 7S0.6: 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, Q.111, M.112, E.113, H.114 Ligands: FMT.5, FMT.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.56, B:Y.56 Hydrogen bonds: B:M.49, B:Y.56, B:E.113, A:N.19 Water bridges: B:Q.111, B:H.114

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

FMT.2: 6 residues within 4Å: Chain A: F.9, H.12 Chain B: F.87, H.114, V.115 Ligands: FMT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.12 Water bridges: A:D.15 FMT.3: 3 residues within 4Å: Chain A: Y.56 Chain B: R.26 Ligands: 7S0.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.56 FMT.4: 5 residues within 4Å: Chain A: I.7, Q.8, F.9 Chain B: H.114, T.118 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.8 Water bridges: B:H.114 FMT.5: 8 residues within 4Å: Chain A: H.12, D.15, V.16, N.19 Chain B: A.50, C.51 Ligands: FMT.2, 7S0.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.12, A:D.15, A:D.15 Water bridges: A:N.19 FMT.7: 6 residues within 4Å: Chain A: F.87, H.114, V.115 Chain B: F.9, H.12 Ligands: FMT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.12 FMT.8: 3 residues within 4Å: Chain A: R.26 Chain B: Y.56 Ligands: 7S0.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.56 FMT.9: 5 residues within 4Å: Chain A: H.114, T.118 Chain B: I.7, Q.8, F.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.8 Water bridges: A:H.114 FMT.10: 8 residues within 4Å: Chain A: A.50, C.51 Chain B: H.12, D.15, V.16, N.19 Ligands: 7S0.1, FMT.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.12, B:D.15 Water bridges: B:N.19

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-8388. 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

Related Entries With Identical Sequence