SMTL ID : 7okd.1

Crystal structure of human BCL6 BTB domain in complex with compound 25

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x VGW: 2-chloranyl-4-[[4-[2-(5-cyclopropylpyrimidin-2-yl)propan-2-ylamino]-1-methyl-2-oxidanylidene-quinolin-6-yl]amino]pyridine-3-carbonitrile(Non-covalent)

VGW.1: 15 residues within 4Å: Chain A: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130, H.131 Chain B: D.32, N.36, R.39, L.40, R.43 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:D.32 Water bridges: B:H.29, B:N.36, B:R.39, B:R.43, A:H.131 Hydrogen bonds: A:M.66, A:A.67, A:E.130 pi-Stacking: A:Y.73 VGW.7: 15 residues within 4Å: Chain A: D.32, N.36, R.39, L.40, R.43 Chain B: M.66, A.67, C.68, S.69, G.70, Y.73, Q.128, M.129, E.130, H.131 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:M.66, B:A.67, B:E.130, B:H.131 Water bridges: B:H.131, A:N.36, A:R.39, A:R.43 pi-Stacking: B:Y.73 Hydrophobic interactions: A:D.32

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

EDO.2: 4 residues within 4Å: Chain A: Y.16, F.17, Q.18, I.24 No protein-ligand interaction detected (PLIP) EDO.3: 1 residues within 4Å: Chain A: Q.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.57 EDO.4: 2 residues within 4Å: Chain A: E.114, I.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.114 EDO.8: 4 residues within 4Å: Chain B: Y.16, F.17, Q.18, I.24 No protein-ligand interaction detected (PLIP) EDO.9: 1 residues within 4Å: Chain B: Q.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.57 EDO.10: 2 residues within 4Å: Chain B: E.114, I.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.114

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

DMS.5: 6 residues within 4Å: Chain A: E.56, F.58, P.95, E.96, C.99 Ligands: DMS.6 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.56 DMS.6: 5 residues within 4Å: Chain A: E.96, C.99, I.100, D.103 Ligands: DMS.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.103 Salt bridges: A:E.96 DMS.11: 6 residues within 4Å: Chain B: E.56, F.58, P.95, E.96, C.99 Ligands: DMS.12 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.56 DMS.12: 5 residues within 4Å: Chain B: E.96, C.99, I.100, D.103 Ligands: DMS.11 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.96

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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