SMTL ID : 7okl.1

Crystal structure of human BCL6 BTB domain in complex with compound 13e

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 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, T.119 Ligands: EDO.12 12 PLIP interactions: 4 interactions with chain B, 8 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 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.13: 11 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 Ligands: EDO.24 12 PLIP interactions: 4 interactions with chain A, 8 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 Hydrogen bonds: B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x VJ5: 2-chloranyl-4-[[1-methyl-2-oxidanylidene-4-[[(1R)-1-pyrimidin-2-ylethyl]amino]quinolin-6-yl]amino]pyridine-3-carbonitrile(Non-covalent)

VJ5.2: 17 residues within 4Å: Chain A: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114, H.115 Chain B: F.10, D.16, N.20, R.23, L.24, R.27 Ligands: DMS.11 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:M.50, A:A.51, A:E.114, B:D.16, B:N.20 Water bridges: A:H.115, B:R.27 pi-Stacking: A:Y.57 Hydrophobic interactions: B:D.16 VJ5.14: 17 residues within 4Å: Chain A: F.10, D.16, 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, H.115 Ligands: DMS.23 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:M.50, B:A.51, B:E.114, A:N.20 Water bridges: B:H.115, B:H.115, A:R.27 pi-Stacking: B:Y.57 Hydrophobic interactions: A:D.16

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

EDO.3: 2 residues within 4Å: Chain A: R.97, E.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.98 Water bridges: A:R.97, A:G.99 EDO.4: 2 residues within 4Å: Chain A: D.74, 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: 4 residues within 4Å: Chain A: F.42, P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.80 EDO.7: 1 residues within 4Å: Chain A: Q.41 No protein-ligand interaction detected (PLIP) EDO.12: 5 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, ALA-TRP-VAL-ILE-PRO-ALA.1 No protein-ligand interaction detected (PLIP) EDO.15: 2 residues within 4Å: Chain B: R.97, E.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.98 Water bridges: B:R.97, B:G.99 EDO.16: 2 residues within 4Å: Chain B: D.74, Y.110 No protein-ligand interaction detected (PLIP) EDO.17: 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.18: 4 residues within 4Å: Chain B: F.42, P.79, E.80, C.83 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.80, B:E.80 EDO.19: 1 residues within 4Å: Chain B: Q.41 No protein-ligand interaction detected (PLIP) EDO.24: 5 residues within 4Å: Chain A: F.123 Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.13, ALA-TRP-VAL-ILE-PRO-ALA.13, ALA-TRP-VAL-ILE-PRO-ALA.13 No protein-ligand interaction detected (PLIP)

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

CL.8: 1 residues within 4Å: Chain A: R.23 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: M.113, H.115, V.116 Ligand excluded by PLIP CL.20: 1 residues within 4Å: Chain B: R.23 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: L.68, S.69, V.70 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: M.113, H.115, V.116 Ligand excluded by PLIP

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

DMS.11: 3 residues within 4Å: Chain A: E.114, H.115 Ligands: VJ5.2 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.114 DMS.23: 3 residues within 4Å: Chain B: E.114, H.115 Ligands: VJ5.14 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.114

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

Related Entries With Identical Sequence