SMTL ID : 7okf.1

Crystal structure of human BCL6 BTB domain in complex with compound 8c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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: 12 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, V.116, T.119 Ligands: EDO.13 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.8, A:I.8, A:Q.9, A:F.10, A:F.10, A:F.10, B:F.88, B:L.94, B:L.94, B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 Water bridges: B:D.118 ALA-TRP-VAL-ILE-PRO-ALA.14: 12 residues within 4Å: Chain A: F.88, R.93, L.94, H.115, V.116, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 Ligands: EDO.26 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.8, B:I.8, B:Q.9, B:F.10, B:F.10, B:F.10, A:F.88, A:L.94, A:L.94, A:T.119 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x VH5: 2-chloranyl-4-[[4-(4-methylpiperazin-1-yl)-2-oxidanylidene-1H-quinolin-6-yl]amino]pyridine-3-carbonitrile(Non-covalent)

VH5.2: 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: DMS.8 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:N.20 Hydrogen bonds: B:R.23, A:M.50, A:G.54, A:E.114 Water bridges: B:R.27, B:R.27, A:E.114 pi-Stacking: A:Y.57 VH5.15: 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: DMS.21 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:M.50, B:G.54, B:E.114, A:R.23 Water bridges: B:E.114, B:E.114, A:R.27, A:R.27 pi-Stacking: B:Y.57 Hydrophobic interactions: A:N.20

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

EDO.3: 3 residues within 4Å: Chain A: D.62, Q.63, L.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.63, A:Q.63, A:L.64 EDO.4: 4 residues within 4Å: Chain A: E.98, I.101, I.124, S.127 1 PLIP interactions: 1 interactions with chain A Water bridges: A:M.102 EDO.5: 2 residues within 4Å: Chain A: V.36, Q.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.41 EDO.6: 3 residues within 4Å: Chain A: Y.57, S.58, T.61 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.61, A:T.61 Water bridges: A:S.58, A:S.58 EDO.7: 2 residues within 4Å: Chain A: E.76, Y.110 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: I.8 Chain B: F.123 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1, ALA-TRP-VAL-ILE-PRO-ALA.1 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.119 EDO.16: 3 residues within 4Å: Chain B: D.62, Q.63, L.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.63, B:Q.63, B:L.64 EDO.17: 4 residues within 4Å: Chain B: E.98, I.101, I.124, S.127 1 PLIP interactions: 1 interactions with chain B Water bridges: B:M.102 EDO.18: 2 residues within 4Å: Chain B: V.36, Q.41 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.41 EDO.19: 3 residues within 4Å: Chain B: Y.57, S.58, T.61 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.61 Water bridges: B:S.58, B:S.58, B:T.61, B:T.61 EDO.20: 2 residues within 4Å: Chain B: E.76, Y.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76 EDO.26: 4 residues within 4Å: Chain A: F.123 Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.14, ALA-TRP-VAL-ILE-PRO-ALA.14 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.119

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

DMS.8: 1 residues within 4Å: Ligands: VH5.2 No protein-ligand interaction detected (PLIP) DMS.9: 3 residues within 4Å: Chain A: P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.10: 2 residues within 4Å: Chain A: R.23, S.26 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.22, A:N.22 DMS.21: 1 residues within 4Å: Ligands: VH5.15 No protein-ligand interaction detected (PLIP) DMS.22: 3 residues within 4Å: Chain B: P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.23: 2 residues within 4Å: Chain B: R.23, S.26 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.22, B:N.22

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

CL.11: 3 residues within 4Å: Chain A: M.113, H.115, V.116 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: M.113, H.115, V.116 Ligand excluded by PLIP CL.25: 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

Lloyd, M.G. et al., Into Deep Water: Optimizing BCL6 Inhibitors by Growing into a Solvated Pocket. J.Med.Chem. (2021)

Release Date

2021-12-08

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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