SMTL ID : 5ftg.1

Human choline kinase a1 in complex with compound 1-[[4-[2-[4-[[4-(dimethylamino)pyridin-1- yl]methyl]phenoxy]ethoxy]phenyl]methyl]-N,N- dimethyl-pyridin-4-amine (compound 10a)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x NBR: 1-[[4-[2-[4-[[4-(dimethylamino)pyridin-1-yl]methyl]phenoxy]ethoxy]phenyl]methyl]-N,N-dimethyl-pyridin-4-amine(Non-covalent)

NBR.1: 15 residues within 4Å: Chain A: N.226, D.227, Q.229, Y.254, E.270, Y.275, E.278, F.282, W.341, W.344, I.354, E.355, F.356, Y.361 Ligands: EDO.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.282, A:F.282, A:W.341, A:W.341, A:W.344, A:W.344, A:I.354, A:F.356, A:Y.361 pi-Stacking: A:Y.275 NBR.12: 15 residues within 4Å: Chain B: N.226, D.227, Q.229, Y.254, E.270, Y.275, E.278, F.282, W.341, W.344, I.354, E.355, F.356, Y.361 Ligands: EDO.20 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.282, B:F.282, B:W.341, B:W.341, B:W.344, B:W.344, B:I.354, B:F.356, B:Y.361 pi-Stacking: B:Y.275

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

EDO.2: 6 residues within 4Å: Chain A: T.137, E.138, L.140, S.141, W.271, K.289 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: W.271, R.288, K.289, Y.290, P.291, T.292, Q.295 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: W.271, M.272, Y.273, D.274, R.284, K.289 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: R.10, Y.13, L.14 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.1, H.33, I.34, S.35, Q.47, S.49, K.63 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: I.120, F.121, P.122 Chain B: E.96, V.99, L.100 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: L.214, E.215, T.217, S.219, Y.259, F.333 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: D.227, Q.229, W.344 Ligands: NBR.1 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: Y.273, A.285, A.364, D.367, A.368 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: M.272, I.287, Y.290, H.338, A.368, H.371, Q.372 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain B: T.137, E.138, L.140, S.141, W.271, K.289 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain B: W.271, R.288, K.289, Y.290, P.291, T.292, Q.295 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain B: W.271, M.272, Y.273, D.274, R.284, K.289 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain B: R.10, Y.13, L.14 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: D.1, H.33, I.34, S.35, Q.47, S.49, K.63 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: E.96, V.99, L.100 Chain B: I.120, F.121, P.122 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: L.214, E.215, T.217, S.219, Y.259, F.333 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: D.227, Q.229, W.344 Ligands: NBR.12 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain B: Y.273, A.285, A.364, D.367, A.368 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain B: M.272, I.287, Y.290, H.338, A.368, H.371, Q.372 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiaffino-Ortega, S. et al., Design, Synthesis, Crystallization and Biological Evaluation of New Symmetrical Biscationic Compounds as Selective Inhibitors of Human Choline Kinase Alpha1 (Chokalpha1). Sci.Rep. (2016)

Release Date

2016-03-23

Peptides

CHOLINE KINASE ALPHA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CHOLINE KINASE ALPHA

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