SMTL ID : 8bi6.1

Crystal structure of human Choline Kinase A in complex with UNC0638

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.16: 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 CIQ: 2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine(Non-covalent)

CIQ.2: 11 residues within 4Å: Chain A: D.306, Q.308, E.349, Y.354, S.355, F.361, W.420, W.423, E.434, F.435, Y.440 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Q.308, A:Y.354, A:Y.354, A:F.361, A:F.361, A:W.420, A:W.423, A:W.423, A:F.435 Water bridges: A:E.349 Salt bridges: A:D.306, A:E.349 pi-Cation interactions: A:W.423 CIQ.17: 9 residues within 4Å: Chain B: G.118, G.119, D.306, Y.333, W.420, W.423, I.433, E.434, F.435 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.420, B:I.433 Salt bridges: B:D.306, B:E.434

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

EDO.3: 5 residues within 4Å: Chain A: Y.352, A.364, A.443, D.446, A.447 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.352, A:Y.352 EDO.4: 7 residues within 4Å: Chain A: T.216, W.350, M.351, D.353, R.363, N.365, K.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.350 Water bridges: A:N.365, A:N.365 EDO.5: 4 residues within 4Å: Chain A: P.360, F.362, R.363, A.364 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.364, A:A.364 EDO.6: 4 residues within 4Å: Chain A: F.250, L.293, E.294, Y.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.293, A:Y.338 EDO.7: 4 residues within 4Å: Chain A: F.449, H.450, R.453 Ligands: EDO.8 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.450, A:H.450, A:R.453, A:R.453 EDO.8: 3 residues within 4Å: Chain A: Y.280, F.449 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.280 Water bridges: A:Y.280 EDO.9: 3 residues within 4Å: Chain A: E.189, R.190, S.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.191 EDO.18: 5 residues within 4Å: Chain B: E.218, L.221, I.224, E.319, K.325 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.218, B:E.218, B:E.319 EDO.19: 6 residues within 4Å: Chain B: Y.352, A.364, I.366, A.443, D.446, A.447 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.352, B:D.446 EDO.20: 2 residues within 4Å: Chain B: H.377, S.380 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.377, B:S.380, B:S.380 EDO.21: 4 residues within 4Å: Chain B: F.208, P.210, S.211, E.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.211, B:S.211 EDO.22: 4 residues within 4Å: Chain B: R.339, L.383, F.386, Q.387 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.339, B:R.339, B:Q.387 Water bridges: B:E.404

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 7 residues within 4Å: Chain A: W.248, T.252, Y.256, E.332, Y.333, S.334 Ligands: PEG.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.256, A:S.334 PEG.11: 7 residues within 4Å: Chain A: L.179, M.183, F.242, F.331, S.334, S.335 Ligands: PEG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.331

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.12: 1 residues within 4Å: Chain A: H.275 No protein-ligand interaction detected (PLIP) IPA.23: 3 residues within 4Å: Chain B: P.140, R.141, K.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.141

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

PO4.13: 7 residues within 4Å: Chain A: R.270, Y.359, A.428, F.435, G.436, Y.437, M.438 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.437, A:M.438 Water bridges: A:K.273, A:K.273, A:Y.359, A:D.439 Salt bridges: A:R.270 PO4.24: 7 residues within 4Å: Chain B: R.270, Y.359, A.428, F.435, G.436, Y.437, M.438 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.359, B:G.436, B:Y.437, B:M.438 Water bridges: B:D.439, B:D.439 Salt bridges: B:R.270 PO4.25: 3 residues within 4Å: Chain B: S.191, G.193, M.327 No protein-ligand interaction detected (PLIP) PO4.26: 3 residues within 4Å: Chain B: A.134, T.135, R.141 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.135, B:T.135, B:T.135 Water bridges: B:T.133 Salt bridges: B:R.141

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

CL.14: 4 residues within 4Å: Chain A: F.265, T.266, E.267, R.270 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.27: 1 residues within 4Å: Chain B: A.188 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 UNC0638. 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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