SMTL ID : 8bi5.1

Crystal structure of human Choline Kinase A in complex with UNC0737

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.309, E.349, Y.352, Y.354 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.309, A:E.309, A:E.349, A:E.349, A:Y.352 MG.9: 4 residues within 4Å: Chain B: E.309, E.349, Y.352, Y.354 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.309, B:E.309, B:E.349, B:E.349, B:Y.352

2 x QQS: 2-cyclohexyl-6-methoxy-~{N}-methyl-~{N}-(1-propan-2-ylpiperidin-4-yl)-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine(Non-covalent)

QQS.2: 9 residues within 4Å: Chain A: R.117, D.306, Y.333, E.349, Y.354, F.361, W.420, W.423, F.435 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.117, A:Y.333, A:F.361, A:W.420, A:W.423 Salt bridges: A:D.306 QQS.10: 12 residues within 4Å: Chain B: D.306, Q.308, E.349, Y.354, S.355, F.361, W.420, W.423, I.433, E.434, F.435, Y.440 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.354, B:Y.354, B:F.361, B:W.420, B:W.423 Hydrogen bonds: B:Q.308 Water bridges: B:D.306 Salt bridges: B:D.306, B:E.349 pi-Cation interactions: B:W.423

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

EDO.3: 3 residues within 4Å: Chain A: Q.207, F.208, I.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.207, A:I.209 EDO.4: 5 residues within 4Å: Chain A: E.218, L.221, I.224, E.319, K.325 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.218, A:E.319 EDO.5: 6 residues within 4Å: Chain A: Y.352, A.364, I.366, A.443, D.446, A.447 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.352, A:Y.352 EDO.11: 6 residues within 4Å: Chain B: Y.352, A.364, I.366, A.443, D.446, A.447 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.352, B:D.446, B:D.446 EDO.12: 4 residues within 4Å: Chain B: F.449, H.450, R.453 Ligands: EDO.14 5 PLIP interactions: 5 interactions with chain B Water bridges: B:D.446, B:D.446, B:H.450, B:R.453, B:R.453 EDO.13: 2 residues within 4Å: Chain B: R.453, K.454 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.453 EDO.14: 3 residues within 4Å: Chain B: Y.280, F.449 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.280 EDO.15: 4 residues within 4Å: Chain B: P.360, F.362, R.363, A.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.364, B:A.364 EDO.16: 6 residues within 4Å: Chain B: L.293, E.294, T.296, P.297, S.298, Y.338 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.296, B:S.298, B:Y.338 EDO.17: 3 residues within 4Å: Chain B: K.247, G.251, T.252 No protein-ligand interaction detected (PLIP)

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 6 residues within 4Å: Chain A: R.270, A.428, F.435, G.436, Y.437, M.438 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.437, A:M.438 Water bridges: A:K.273, A:D.439 Salt bridges: A:R.270 PO4.18: 2 residues within 4Å: Chain B: R.212, D.215 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.212 Salt bridges: B:R.212 PO4.19: 6 residues within 4Å: Chain B: R.270, Y.359, F.435, G.436, Y.437, M.438 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.359, B:F.435, B:M.438 Water bridges: B:K.273, B:D.439 Salt bridges: B:R.270

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

CL.7: 2 residues within 4Å: Chain A: N.288, K.452 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: S.334 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: F.265, T.266, E.267, R.270 Ligand excluded by PLIP CL.21: 1 residues within 4Å: Chain B: R.453 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: L.179, F.242, S.334 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Crystal structure of human Choline Kinase A in complex with UNC0737. To Be Published

Release Date

2023-11-15

Peptides

Choline kinase alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Choline kinase alpha

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