SMTL ID : 7q7s.1

Crystal structure of human BCL6 BTB domain in complex with compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 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, R.93, L.94, H.115, T.119 14 PLIP interactions: 4 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:L.94, B:T.119, A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.10: 10 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, A:T.119, B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x 97S: 2-chloranyl-4-[[4-(ethylamino)-1,3-dimethyl-2-oxidanylidene-quinolin-6-yl]amino]pyridine-3-carbonitrile(Non-covalent)

97S.2: 14 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Chain B: N.20, R.23, L.24, R.27 Ligands: CL.8 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:E.114, B:N.20 Hydrogen bonds: A:M.50, A:E.114, B:R.23 Water bridges: A:G.54, A:Q.112, B:R.27, B:R.27 pi-Stacking: A:Y.57 97S.11: 14 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, Q.112, M.113, E.114 Ligands: CL.17 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:N.20, B:E.114 Hydrogen bonds: A:R.23, B:M.50, B:E.114 Water bridges: A:R.27, A:R.27, B:G.54, B:Q.112 pi-Stacking: B:Y.57

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

EDO.3: 3 residues within 4Å: Chain A: V.70, I.71, N.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.70, A:N.72, A:N.72 EDO.4: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: E.98, I.101, I.124 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.98, A:E.98, A:M.102 EDO.6: 3 residues within 4Å: Chain A: D.62, Q.63, L.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.63, A:L.64 EDO.7: 4 residues within 4Å: Chain A: D.28, L.30, T.31, R.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.28, A:T.31, A:T.31, A:R.43 Water bridges: A:D.28 EDO.12: 3 residues within 4Å: Chain B: V.70, I.71, N.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.70, B:N.72, B:N.72 EDO.13: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain B: E.98, I.101, I.124 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.98, B:E.98, B:M.102 EDO.15: 3 residues within 4Å: Chain B: D.62, Q.63, L.64 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:L.64 EDO.16: 4 residues within 4Å: Chain B: D.28, L.30, T.31, R.43 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.28, B:T.31, B:R.43

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

CL.8: 4 residues within 4Å: Chain A: M.113, H.115, V.116 Ligands: 97S.2 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: M.113, H.115, V.116 Ligands: 97S.11 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: L.68, S.69, V.70 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davis, O.A. et al., Optimizing Shape Complementarity Enables the Discovery of Potent Tricyclic BCL6 Inhibitors. J.Med.Chem. (2022)

Release Date

2022-06-15

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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