SMTL ID : 2xnn.1

Structure of Nek2 bound to CCT242430

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x 430: 5-(1H-benzimidazol-1-yl)-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide(Non-covalent)

430.1: 16 residues within 4Å: Chain A: I.14, G.15, C.22, V.35, K.37, M.86, E.87, Y.88, C.89, G.92, D.93, A.145, N.146, F.148, G.158, D.159 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.14, A:Y.88, A:D.93, A:F.148 Hydrogen bonds: A:C.89, A:N.146, A:D.159, A:D.159 pi-Stacking: A:F.148 pi-Cation interactions: A:K.37

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

CL.2: 2 residues within 4Å: Chain A: R.234, R.235 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: R.105, Y.107 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: P.65, N.154, H.277 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: S.261, V.262 Ligand excluded by PLIP CL.12: 1 residues within 4Å: Chain A: E.230 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: P.144, Y.181, Y.182, E.208, P.214 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.208 EDO.7: 5 residues within 4Å: Chain A: I.247, R.250, P.260, E.264, N.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.250, A:E.264, A:N.268 EDO.8: 3 residues within 4Å: Chain A: L.272, E.273, H.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.274 EDO.9: 4 residues within 4Å: Chain A: K.152, Q.153, H.278, H.279 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.278 Water bridges: A:R.115, A:H.278 EDO.10: 4 residues within 4Å: Chain A: A.5, Y.8, V.10, W.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.5, A:V.10 EDO.11: 3 residues within 4Å: Chain A: P.237, Y.238, R.239 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.238, A:R.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Solanki, S. et al., Benzimidazole Inhibitors Induce a Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (Nek2) without Binding to the Back Pocket and Reveal a Nonlinear Structure-Activity Relationship. J.Med.Chem. (2011)

Release Date

2011-03-30

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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