SMTL ID : 7okm.1

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

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: 10 residues within 4Å: Chain A: C.7, I.8, Q.9, F.10, T.11 Chain B: F.88, L.94, H.115, T.119 Ligands: EDO.10 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.88, B:L.94, B:L.94, A:I.8, A:F.10, A:F.10 Water bridges: B:T.119 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.11: 10 residues within 4Å: Chain A: F.88, L.94, H.115, T.119 Chain B: C.7, I.8, Q.9, F.10, T.11 Ligands: EDO.20 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:F.88, A:L.94, A:L.94, B:I.8, B:F.10, B:F.10 Hydrogen bonds: A:T.119, B:Q.9, B:Q.9, B:T.11 Water bridges: B:T.11

2 x VJ2: 2-chloranyl-4-[[1-methyl-2-oxidanylidene-4-(2-pyrimidin-2-ylpropan-2-ylamino)quinolin-6-yl]amino]pyridine-3-carbonitrile(Non-covalent)

VJ2.2: 16 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: D.16, N.20, R.23, L.24, R.27 Ligands: EDO.13 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:M.50, A:A.51, A:E.114, B:D.16 Water bridges: A:H.115, B:N.20, B:R.27, B:R.27 pi-Stacking: A:Y.57 Hydrophobic interactions: B:D.16 VJ2.12: 16 residues within 4Å: Chain A: 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: EDO.3 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:D.16 Water bridges: A:N.20, A:R.27, B:Y.57, B:H.115 Hydrogen bonds: B:M.50, B:A.51, B:E.114 pi-Stacking: B:Y.57

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

EDO.3: 6 residues within 4Å: Chain A: F.10, R.12, H.13, D.16 Chain B: H.115 Ligands: VJ2.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.12 EDO.4: 3 residues within 4Å: Chain A: D.74, I.77, Y.110 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.110 EDO.5: 4 residues within 4Å: Chain A: E.98, I.101, I.124, S.127 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.98, A:M.102 EDO.6: 2 residues within 4Å: Chain A: D.62, Q.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.63 EDO.7: 4 residues within 4Å: Chain A: V.36, S.38, R.39, L.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.38, A:R.39, A:L.73 EDO.10: 4 residues within 4Å: Chain A: I.8 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.13: 6 residues within 4Å: Chain A: H.115 Chain B: F.10, R.12, H.13, D.16 Ligands: VJ2.2 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.12, B:D.16 EDO.14: 3 residues within 4Å: Chain B: D.74, I.77, Y.110 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.110 EDO.15: 4 residues within 4Å: Chain B: E.98, I.101, I.124, S.127 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.98, B:M.102 EDO.16: 2 residues within 4Å: Chain B: D.62, Q.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.63 EDO.17: 4 residues within 4Å: Chain B: V.36, S.38, R.39, L.73 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.38, B:R.39, B:L.73 EDO.20: 4 residues within 4Å: Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.11, ALA-TRP-VAL-ILE-PRO-ALA.11, ALA-TRP-VAL-ILE-PRO-ALA.11 No protein-ligand interaction detected (PLIP)

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

DMS.8: 3 residues within 4Å: Chain A: P.79, E.80, C.83 No protein-ligand interaction detected (PLIP) DMS.18: 3 residues within 4Å: Chain B: P.79, E.80, C.83 No protein-ligand interaction detected (PLIP)

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

CL.9: 3 residues within 4Å: Chain A: L.68, S.69, V.70 Ligand excluded by PLIP CL.19: 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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