SMTL ID : 2xnm.1

STRUCTURE OF NEK2 BOUND TO CCT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x WGZ: 5-{6-[(1-METHYLPIPERIDIN-4-YL)OXY]-1H-BENZIMIDAZOL-1-YL}-3-{(1R)-1-[2-(TRIFLUOROMETHYL)PHENYL]ETHOXY}THIOPHENE-2-CARBOXAMIDE(Non-covalent)

WGZ.1: 18 residues within 4Å: Chain A: I.14, G.15, C.22, V.35, K.37, E.87, Y.88, C.89, G.92, D.93, S.96, A.145, F.148, G.158, D.159, L.162, A.163, L.166 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.14, A:Y.88, A:F.148, A:L.166 Hydrogen bonds: A:C.89, A:D.159, A:D.159 Water bridges: A:S.96, A:N.146 pi-Stacking: A:F.148 pi-Cation interactions: A:K.37

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

EDO.2: 3 residues within 4Å: Chain A: K.152, Q.153, H.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.278 Water bridges: A:R.115, A:Q.153, A:H.278 EDO.3: 4 residues within 4Å: Chain A: I.247, E.264, I.265, N.268 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.264, A:N.268 EDO.4: 3 residues within 4Å: Chain A: D.242, E.243, E.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.243 EDO.5: 4 residues within 4Å: Chain A: Y.238, R.239, Y.240, S.241 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.238, A:Y.240, A:D.242, A:D.242 EDO.6: 2 residues within 4Å: Chain A: F.112, Q.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.153 EDO.7: 5 residues within 4Å: Chain A: R.234, R.235, I.236, P.237, Y.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.234 Water bridges: A:R.234 EDO.8: 5 residues within 4Å: Chain A: P.144, Y.181, Y.182, E.208, P.214 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: E.195, K.196, S.261, V.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.262

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

CL.10: 2 residues within 4Å: Chain A: R.105, Y.107 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: D.109, E.110, R.239 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: P.65, N.154, H.277, H.279 Ligand excluded by PLIP

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.12: 6 residues within 4Å: Chain A: H.128, R.130, Y.193, N.194, E.195, D.198 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.128, A:R.130, A:R.130, A:N.194, A:N.194 Water bridges: A:D.198

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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