SMTL ID : 7oki.1

Crystal structure of human BCL6 BTB domain in complex with compound 12b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 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.7 14 PLIP interactions: 5 interactions with chain B, 9 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, A:F.10 Water bridges: B:R.93 Hydrogen bonds: A:Q.9, A:Q.9, A:T.11, A:T.11 ALA-TRP-VAL-ILE-PRO-ALA.8: 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.14 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.8, B:I.8, B:Q.9, 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, A:R.93

2 x VHZ: (2R)-2-[[6-[(2-chloranyl-3-cyano-pyridin-4-yl)amino]-2-oxidanylidene-1H-quinolin-4-yl]amino]-N-methyl-propanamide(Non-covalent)

VHZ.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: H.13, D.16, V.17, N.20, R.23, L.24, R.27 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:D.16, B:V.17, B:N.20 Hydrogen bonds: B:D.16, B:N.20, B:R.27, A:M.50, A:A.51, A:G.54, A:Q.112, A:E.114 Water bridges: B:H.13, B:H.13, A:V.116 pi-Stacking: A:Y.57 VHZ.9: 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, H.115 13 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:D.16, A:V.17, A:N.20 Hydrogen bonds: A:N.20, A:R.27, B:M.50, B:A.51, B:G.54, B:Q.112, B:E.114 Water bridges: B:Y.57, B:V.116 pi-Stacking: B:Y.57

6 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: 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.7: 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.10: 2 residues within 4Å: Chain B: R.97, E.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.98 EDO.11: 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.14: 4 residues within 4Å: Chain B: I.8 Ligands: ALA-TRP-VAL-ILE-PRO-ALA.8, ALA-TRP-VAL-ILE-PRO-ALA.8, ALA-TRP-VAL-ILE-PRO-ALA.8 No protein-ligand interaction detected (PLIP)

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

DMS.5: 3 residues within 4Å: Chain A: E.98, I.101, M.102 No protein-ligand interaction detected (PLIP) DMS.6: 3 residues within 4Å: Chain A: P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.40 DMS.12: 3 residues within 4Å: Chain B: E.98, I.101, M.102 No protein-ligand interaction detected (PLIP) DMS.13: 3 residues within 4Å: Chain B: P.79, E.80, C.83 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.40

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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