SMTL ID : 2xno.1

Structure of Nek2 bound to CCT243779

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x ED8: 5-{6-[(1-methylpiperidin-4-yl)oxy]-1H-benzimidazol-1-yl}-3-{[2-(trifluoromethyl)benzyl]oxy}thiophene-2-carboxamide(Non-covalent)

ED8.1: 16 residues within 4Å: Chain A: I.14, G.15, C.22, V.35, K.37, M.86, E.87, Y.88, C.89, D.93, S.96, A.145, F.148, G.158, D.159 Ligands: EDO.15 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.88, A:F.148, A:F.148 Hydrogen bonds: A:K.37, A:C.89, A:S.96, A:D.159, A:D.159, A:D.159 Salt bridges: A:D.93 pi-Stacking: A:F.148

2 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: 3 residues within 4Å: Chain A: D.109, E.110, R.239 Ligand excluded by PLIP

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

EDO.4: 3 residues within 4Å: Chain A: K.152, Q.153, H.278 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.153 Water bridges: A:R.115, A:H.278, A:H.278 EDO.5: 3 residues within 4Å: Chain A: Y.181, E.208, P.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.208 EDO.6: 5 residues within 4Å: Chain A: E.195, K.196, I.199, S.261, V.262 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.262 Water bridges: A:H.128 EDO.7: 6 residues within 4Å: Chain A: R.234, R.235, I.236, P.237, Y.238 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.234 Water bridges: A:R.234 EDO.8: 3 residues within 4Å: Chain A: R.235, Y.238, D.242 No protein-ligand interaction detected (PLIP) EDO.9: 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.10: 5 residues within 4Å: Chain A: L.266, I.271, L.272, E.273, H.276 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain A: Y.207, A.211, R.234, R.235, I.236, P.237 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.234 EDO.12: 2 residues within 4Å: Chain A: H.277, H.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.277 EDO.15: 4 residues within 4Å: Chain A: Y.19, K.37, D.159 Ligands: ED8.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.159 EDO.16: 2 residues within 4Å: Chain A: E.55, F.160 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: L.58, L.59, R.140, D.159, F.160 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.159, A:F.160

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.14: 6 residues within 4Å: Chain A: P.65, N.154, K.156, H.277, H.278, H.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.277

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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