SMTL ID : 7rv1.1

Crystal structure of the BCL6 BTB domain in complex with OICR-8826

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-dimer

Ligands

2 x 7RH: (E)-3-(7-(2-((3-chloropyridin-4-yl)amino)-2-oxoethyl)-3-(3-(1-methyl-1H-pyrazol-4-yl)prop-2-yn-1-yl)-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)acrylamide(Non-covalent)

7RH.1: 20 residues within 4Å: Chain A: M.49, A.50, C.51, S.52, G.53, Y.56, F.87, M.108, Q.111, M.112, E.113, H.114, V.115, V.116 Chain B: F.9, H.12, N.19, R.22, L.23, R.26 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:N.19, A:M.49, A:E.113, A:H.114, A:V.115 Water bridges: B:R.26 Hydrophobic interactions: A:Y.56, A:Q.111, A:M.112, A:E.113 7RH.5: 20 residues within 4Å: Chain A: F.9, H.12, N.19, R.22, L.23, R.26 Chain B: M.49, A.50, C.51, S.52, G.53, Y.56, F.87, M.108, Q.111, M.112, E.113, H.114, V.115, V.116 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.56, B:Q.111, B:M.112, B:E.113 Hydrogen bonds: B:M.49, B:E.113, B:E.113, B:H.114, B:V.115, A:N.19 Water bridges: A:R.26

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

SO4.2: 4 residues within 4Å: Chain A: Q.62, R.65 Chain B: R.26, I.28 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Water bridges: B:R.26, B:R.26, A:R.65, A:R.65 Salt bridges: A:R.65 SO4.3: 5 residues within 4Å: Chain A: D.27, I.28, L.29, T.30 Chain B: R.65 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Water bridges: B:Q.62, B:R.65, B:R.65, A:T.30, A:T.30 Salt bridges: B:R.65 Hydrogen bonds: A:D.27, A:L.29 SO4.6: 4 residues within 4Å: Chain A: R.26, I.28 Chain B: Q.62, R.65 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.65, B:R.65, A:R.26, A:R.26 Salt bridges: B:R.65 SO4.7: 5 residues within 4Å: Chain A: R.65 Chain B: D.27, I.28, L.29, T.30 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Water bridges: A:Q.62, A:R.65, A:R.65, B:T.30, B:T.30 Salt bridges: A:R.65 Hydrogen bonds: B:D.27, B:L.29

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

DMS.4: 2 residues within 4Å: Chain A: Q.62, L.63 No protein-ligand interaction detected (PLIP) DMS.8: 2 residues within 4Å: Chain B: Q.62, L.63 No protein-ligand interaction detected (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-8826. 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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