SMTL ID : 5eqy.1

Crystal structure of choline kinase alpha-1 bound by 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile (compound 65)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x 5RA: 5-[(4-methyl-1,4-diazepan-1-yl)methyl]-2-[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]benzenecarbonitrile(Non-covalent)

5RA.1: 12 residues within 4Å: Chain A: D.250, Q.252, Y.277, E.293, Y.298, F.305, W.364, W.367, I.377, E.378, F.379, Y.384 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.298, A:W.364, A:I.377, A:F.379, A:F.379, A:F.379 Hydrogen bonds: A:Q.252 Salt bridges: A:D.250, A:D.250, A:E.293, A:E.378 pi-Stacking: A:Y.298 5RA.2: 12 residues within 4Å: Chain B: D.250, Q.252, Y.277, E.293, Y.298, F.305, W.364, W.367, I.377, E.378, F.379, Y.384 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.298, B:F.305, B:W.364, B:I.377, B:F.379, B:F.379, B:F.379 Hydrogen bonds: B:Q.252 Water bridges: B:N.255 Salt bridges: B:D.250, B:D.250, B:E.293 pi-Stacking: B:Y.298 pi-Cation interactions: B:W.367

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zech, S.G. et al., Novel Small Molecule Inhibitors of Choline Kinase Identified by Fragment-Based Drug Discovery. J.Med.Chem. (2016)

Release Date

2016-01-06

Peptides

Choline kinase alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Choline kinase alpha

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