SMTL ID : 6tom.1

Crystal structure of human BCL6 BTB domain in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x NQZ: 5-[[2-[(3~{S},5~{R})-4,4-bis(fluoranyl)-3,5-dimethyl-piperidin-1-yl]-5-chloranyl-pyrimidin-4-yl]amino]-1-methyl-3-(3-methyl-3-oxidanyl-butyl)benzimidazol-2-one(Non-covalent)

NQZ.1: 15 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130, H.131 Chain B: D.32, N.36, R.39, L.40, R.43 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.73, B:D.32 Hydrogen bonds: A:M.66, A:Y.73, A:E.130 Water bridges: A:H.131, B:H.29, B:N.36, B:N.36 NQZ.5: 15 residues within 4Å: Chain A: D.32, N.36, R.39, L.40, R.43 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130, H.131 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.73, A:D.32 Hydrogen bonds: B:M.66, B:E.130 Water bridges: B:H.131, A:N.36, A:N.36

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: Y.16, F.17, Q.18, I.24 No protein-ligand interaction detected (PLIP) EDO.3: 6 residues within 4Å: Chain A: S.54, P.91, E.92, I.93, N.94, P.95 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.54, A:P.91, A:N.94 EDO.4: 4 residues within 4Å: Chain A: E.130, V.133, D.134, R.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.134 EDO.6: 4 residues within 4Å: Chain B: Y.16, F.17, Q.18, I.24 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain B: S.54, P.91, E.92, I.93, N.94, P.95 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.54, B:P.91, B:N.94 EDO.8: 4 residues within 4Å: Chain B: E.130, V.133, D.134, R.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.134

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bellenie, B.R. et al., AchievingIn VivoTarget Depletion through the Discovery and Optimization of Benzimidazolone BCL6 Degraders. J.Med.Chem. (2020)

Release Date

2020-04-22

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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