SMTL ID : 4b9d.1

Crystal Structure of Human NIMA-related Kinase 1 (NEK1) with inhibitor.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x CK7: [4-(2-AMINO-4-METHYL-THIAZOL-5-YL)-PYRIMIDIN-2-YL]-(3-NITRO-PHENYL)-AMINE(Non-covalent)

CK7.1: 10 residues within 4Å: Chain A: I.32, A.40, V.53, M.102, D.103, Y.104, C.105, G.108, D.109, F.157 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.53, A:Y.104 Hydrogen bonds: A:I.32, A:C.105, A:C.105 Water bridges: A:A.40 pi-Stacking: A:F.157 CK7.4: 12 residues within 4Å: Chain B: I.32, G.33, A.40, V.53, K.55, M.102, D.103, Y.104, C.105, G.108, D.109, F.157 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.53, B:Y.104, B:F.157, B:F.157 Hydrogen bonds: B:K.55, B:C.105, B:C.105 Water bridges: B:K.55 pi-Stacking: B:F.157

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

CL.2: 3 residues within 4Å: Chain A: N.264, P.265, R.266 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: H.142, N.204, S.270, V.271 Ligand excluded by PLIP CL.5: 5 residues within 4Å: Chain B: H.142, N.204, I.208, S.270, V.271 Ligand excluded by PLIP

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

EDO.6: 3 residues within 4Å: Chain B: K.81, H.82, P.83 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Melo-Hanchuk, T.D. et al., NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin. Sci Rep (2017)

Release Date

2012-09-19

Peptides

SERINE/THREONINE-PROTEIN KINASE NEK1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SERINE/THREONINE-PROTEIN KINASE NEK1

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