SMTL ID : 7t0u.2 (1 other biounit)

Crystal structure of the BCL6 BTB domain in complex with OICR-12387

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: L.29, D.31, H.44, K.45, T.46 Chain B: L.29, D.31, H.44, K.45, T.46 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:D.31, A:D.31, A:K.45, A:T.46, B:D.31, B:K.45, B:T.46

2 x E3I: 3-chloro-5-{7-[2-({5-chloro-2-[(2S)-2-methyl-4-(oxetan-3-yl)piperazin-1-yl]pyridin-4-yl}amino)-2-oxoethyl]-3-methyl-4-oxo-2-(trifluoromethyl)-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl}-2-hydroxybenzamide(Non-covalent)

E3I.2: 19 residues within 4Å: Chain A: M.49, A.50, C.51, S.52, G.53, Y.56, F.87, Q.111, M.112, E.113, H.114, V.115 Chain B: F.9, H.12, D.15, V.16, N.19, R.22, L.23 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.56 Hydrogen bonds: A:M.49, A:E.113, A:H.114, A:V.115, B:H.12, B:N.19 Halogen bonds: B:H.12 E3I.3: 20 residues within 4Å: Chain A: F.9, H.12, D.15, V.16, N.19, R.22, L.23, R.26 Chain B: M.49, A.50, C.51, S.52, G.53, Y.56, F.87, Q.111, M.112, E.113, H.114, V.115 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.56 Hydrogen bonds: B:M.49, B:E.113, B:H.114, B:V.115, A:H.12, A:N.19, A:R.26 Halogen bonds: A:H.12

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 5 residues within 4Å: Chain A: R.65 Chain B: D.27, I.28, L.29, T.30 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.29, A:R.65

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: H.114 Chain B: Q.8, F.9, T.10, R.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.10 Water bridges: B:R.11, A:H.114 Salt bridges: A:H.114

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

CL.6: 3 residues within 4Å: Chain B: Q.62, R.65, N.66 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuntz, D.A. et al., Crystal structure of the BCL6 BTB domain in complex with OICR-12387. To Be Published

Release Date

2022-11-09

Peptides

Isoform 2 of B-cell lymphoma 6 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isoform 2 of B-cell lymphoma 6 protein

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