SMTL ID : 5m53.1

Nek2 bound to arylaminopurine inhibitor 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 7GJ: 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N},~{N}-dimethyl-benzamide(Non-covalent)

7GJ.1: 17 residues within 4Å: Chain A: I.14, G.17, Y.19, C.22, V.35, K.37, V.68, M.86, E.87, Y.88, C.89, E.90, G.92, D.93, F.148, D.159 Ligands: PEG.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.14, A:Y.88 Hydrogen bonds: A:K.37, A:K.37, A:C.89, A:C.89 pi-Stacking: A:F.148, A:F.148

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

PEG.2: 6 residues within 4Å: Chain A: Y.12, T.13, I.14, K.24, Y.88 Ligands: 7GJ.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.12, A:T.13, A:Y.88 PEG.3: 8 residues within 4Å: Chain A: L.59, T.136, V.137, L.138, H.139, R.140, F.160, G.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.138, A:R.140

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

EDO.4: 5 residues within 4Å: Chain A: Y.19, K.37, D.159, F.160, L.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.159, A:F.160 Water bridges: A:F.160 EDO.5: 8 residues within 4Å: Chain A: S.18, Y.19, D.141, N.146, D.159, F.160, G.161, L.162 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.141, A:D.141, A:N.146, A:L.162 Water bridges: A:L.162 EDO.6: 4 residues within 4Å: Chain A: E.246, T.249, R.250, N.253 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.246, A:N.253, A:N.253 EDO.7: 9 residues within 4Å: Chain A: Y.207, A.211, M.213, R.234, R.235, I.236, P.237 Ligands: PO4.12, PO4.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.207 Water bridges: A:Y.107 EDO.8: 6 residues within 4Å: Chain A: R.250, Y.257, H.258, R.259, P.260, E.264 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.250, A:Y.257 EDO.9: 6 residues within 4Å: Chain A: P.185, E.186, M.191, L.254, K.255, D.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.186, A:D.256 Water bridges: A:N.194

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

PO4.10: 4 residues within 4Å: Chain A: R.105, Q.106, Y.107, L.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.107 Salt bridges: A:R.105 PO4.11: 3 residues within 4Å: Chain A: D.109, E.110, R.239 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.110 Water bridges: A:E.110, A:E.110, A:E.111, A:R.239 Salt bridges: A:R.239 PO4.12: 8 residues within 4Å: Chain A: Y.207, M.213, P.214, P.215, F.216, F.233, R.234 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.214, A:R.234 PO4.13: 6 residues within 4Å: Chain A: R.234, R.235, I.236, P.237, Y.238 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.238 Salt bridges: A:R.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coxon, C.R. et al., Structure-guided design of purine-based probes for selective Nek2 inhibition. Oncotarget (2017)

Release Date

2016-11-09

Peptides

Serine/threonine-protein kinase Nek2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serine/threonine-protein kinase Nek2

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