SMTL ID : 7okg.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 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: 11 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 14 PLIP interactions: 10 interactions with chain A, 4 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 ALA-TRP-VAL-ILE-PRO-ALA.10: 11 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 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 VHB: 2-chloranyl-4-[[4-(1-methylpyrazol-4-yl)-2-oxidanylidene-1H-quinolin-6-yl]amino]pyridine-3-carbonitrile(Non-covalent)

VHB.2: 17 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: H.13, D.16, V.17, N.20, R.23, L.24, R.27 Ligands: CL.8 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.57, B:N.20 Hydrogen bonds: A:M.50, A:G.54, A:E.114, B:H.13, B:R.23 pi-Stacking: A:Y.57 Water bridges: B:R.27, B:R.27 VHB.11: 17 residues within 4Å: Chain A: H.13, D.16, V.17, 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 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.57, A:N.20 Hydrogen bonds: B:M.50, B:G.54, B:E.114, A:R.23 pi-Stacking: B:Y.57 Water bridges: A:R.27, A:R.27

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

EDO.3: 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.4: 3 residues within 4Å: Chain A: D.74, E.76, Y.110 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.74 EDO.5: 3 residues within 4Å: Chain A: E.98, I.101, I.124 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.98, A:M.102 EDO.6: 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.7: 2 residues within 4Å: Chain A: Q.41, V.70 No protein-ligand interaction detected (PLIP) EDO.12: 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.13: 3 residues within 4Å: Chain B: D.74, E.76, Y.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.74 EDO.14: 3 residues within 4Å: Chain B: E.98, I.101, I.124 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.98, B:M.102 EDO.15: 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.16: 2 residues within 4Å: Chain B: Q.41, V.70 No protein-ligand interaction detected (PLIP)

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

CL.8: 4 residues within 4Å: Chain A: M.113, H.115, V.116 Ligands: VHB.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: VHB.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

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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