SMTL ID : 2xnp.1

Structure of Nek2 bound to CCT244858

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x WCX: 4-{5-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-2-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}BENZAMIDE(Non-covalent)

WCX.1: 19 residues within 4Å: Chain A: I.14, G.15, Y.19, C.22, V.35, K.37, V.68, M.86, E.87, Y.88, C.89, E.90, G.92, D.93, A.145, F.148, G.158, D.159, F.160 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.14, A:V.68, A:Y.88, A:F.148, A:F.160 Hydrogen bonds: A:K.37, A:C.89, A:D.159, A:D.159 Water bridges: A:D.93 pi-Stacking: A:F.148 Halogen bonds: A:I.14, A:Y.19

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

CL.2: 2 residues within 4Å: Chain A: R.105, Y.107 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: N.154, H.277, H.278, H.279 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: Y.207, P.215, F.233, R.234 Ligand excluded by PLIP CL.9: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.5: 5 residues within 4Å: Chain A: P.144, Y.181, Y.182, E.208, P.214 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.208, A:E.208 EDO.6: 3 residues within 4Å: Chain A: D.242, E.243, E.246 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.242, A:D.242 EDO.7: 2 residues within 4Å: Chain A: K.152, Q.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.278 Water bridges: A:R.115, A:H.278 EDO.8: 5 residues within 4Å: Chain A: E.195, K.196, S.261, V.262, E.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.262 EDO.10: 1 residues within 4Å: Chain A: L.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.266

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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