SMTL ID : 7oke.1

Crystal structure of human BCL6 BTB domain in complex with compound 2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 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: 13 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.8, EDO.12 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.13: 13 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.20, EDO.24 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 VHQ: 2-chloranyl-4-[(1-methyl-2-oxidanylidene-quinolin-6-yl)amino]pyridine-3-carbonitrile(Non-covalent)

VHQ.2: 13 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 Ligands: CL.9 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:N.20, A:Y.57 Hydrogen bonds: A:M.50, A:E.114 VHQ.14: 13 residues within 4Å: Chain A: N.20, R.23, L.24 Chain B: M.50, A.51, C.52, S.53, G.54, Y.57, Q.112, M.113, E.114 Ligands: CL.21 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.57, A:N.20 Hydrogen bonds: B:M.50, B:E.114

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

EDO.3: 2 residues within 4Å: Chain A: R.97, E.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.98 EDO.4: 2 residues within 4Å: Chain A: E.76, Y.110 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: E.40, F.42, P.79, E.80, C.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.40 Water bridges: A:E.80 EDO.6: 4 residues within 4Å: Chain A: R.25, F.42, R.43, L.86 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.25, A:R.25, A:Q.41, A:R.43 EDO.7: 3 residues within 4Å: Chain A: L.68, S.69, V.70 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.69, A:V.70 EDO.8: 4 residues within 4Å: Chain A: D.5, S.6, C.7 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.7 Water bridges: A:C.7 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 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.119 EDO.15: 2 residues within 4Å: Chain B: R.97, E.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.98 EDO.16: 2 residues within 4Å: Chain B: E.76, Y.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76 EDO.17: 5 residues within 4Å: Chain B: E.40, F.42, P.79, E.80, C.83 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.40 Water bridges: B:E.40, B:E.80, B:E.80 EDO.18: 4 residues within 4Å: Chain B: R.25, F.42, R.43, L.86 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.25, B:R.25, B:Q.41, B:R.43 EDO.19: 3 residues within 4Å: Chain B: L.68, S.69, V.70 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.69, B:V.70 EDO.20: 4 residues within 4Å: Chain B: D.5, S.6, C.7 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.7 Water bridges: B:C.7 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 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.119

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

CL.9: 4 residues within 4Å: Chain A: M.113, H.115, V.116 Ligands: VHQ.2 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: M.113, H.115, V.116 Ligands: VHQ.14 Ligand excluded by PLIP

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

DMS.10: 4 residues within 4Å: Chain A: V.34, V.36, Q.41, V.70 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain A: E.98, I.101, M.102 No protein-ligand interaction detected (PLIP) DMS.22: 4 residues within 4Å: Chain B: V.34, V.36, Q.41, V.70 No protein-ligand interaction detected (PLIP) DMS.23: 3 residues within 4Å: Chain B: E.98, I.101, M.102 No protein-ligand interaction detected (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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