SMTL ID : 6tog.1

Crystal structure of human BCL6 BTB domain in complex with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

2 x ALA- TRP- VAL- ILE- PRO- ALA: ALA-TRP-VAL-ILE-PRO-ALA(Non-covalent)

ALA-TRP-VAL-ILE-PRO-ALA.1: 10 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, L.94, H.115, V.116, T.119 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10, B:F.88, B:L.94, B:L.94 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11 Water bridges: A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.5: 10 residues within 4Å: Chain A: F.88, L.94, H.115, V.116, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 12 PLIP interactions: 8 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10, A:F.88, A:L.94, A:L.94 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11, A:T.119

2 x NQH: 2-chloranyl-4-(cyclopropylmethylamino)pyridine-3-carbonitrile(Non-covalent)

NQH.2: 10 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57 Chain B: N.20, R.23, L.24, R.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.50 pi-Stacking: A:Y.57 NQH.6: 10 residues within 4Å: Chain A: N.20, R.23, L.24, R.27 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.50 pi-Stacking: B:Y.57

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

DMS.3: 3 residues within 4Å: Chain A: R.23, S.26, R.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.26 DMS.7: 3 residues within 4Å: Chain B: R.23, S.26, R.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.26

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

CL.4: 4 residues within 4Å: Chain A: F.88, M.113, H.115, V.116 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: F.88, M.113, H.115, V.116 Ligand excluded by PLIP

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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