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

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin.

Melo-Hanchuk, T.D.Slepicka, P.F.Meirelles, G.V.Basei, F.L.Lovato, D.V.Granato, D.C.Pauletti, B.A.Domingues, R.R.Leme, A.F.P.Pelegrini, A.L.Lenz, G.Knapp, S.Elkins, J.M.Kobarg, J.

(2017) Sci Rep 7: 5445-5445

  • DOI: https://doi.org/10.1038/s41598-017-05325-w
  • Primary Citation of Related Structures:  
    4APC, 4B9D

  • PubMed Abstract: 

    NEK family kinases are serine/threonine kinases that have been functionally implicated in the regulation of the disjunction of the centrosome, the assembly of the mitotic spindle, the function of the primary cilium and the DNA damage response. NEK1 shows pleiotropic functions and has been found to be mutated in cancer cells, ciliopathies such as the polycystic kidney disease, as well as in the genetic diseases short-rib thoracic dysplasia, Mohr-syndrome and amyotrophic lateral sclerosis. NEK1 is essential for the ionizing radiation DNA damage response and priming of the ATR kinase and of Rad54 through phosphorylation. Here we report on the structure of the kinase domain of human NEK1 in its apo- and ATP-mimetic inhibitor bound forms. The inhibitor bound structure may allow the design of NEK specific chemo-sensitizing agents to act in conjunction with chemo- or radiation therapy of cancer cells. Furthermore, we characterized the dynamic protein interactome of NEK1 after DNA damage challenge with cisplatin. Our data suggest that NEK1 and its interaction partners trigger the DNA damage pathways responsible for correcting DNA crosslinks.

  • Organizational Affiliation

    Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
350Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PY6 (Homo sapiens)
Explore Q96PY6 
Go to UniProtKB:  Q96PY6
GTEx:  ENSG00000137601 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PY6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.36α = 90
b = 93.66β = 90
c = 164.96γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-19
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references, Structure summary
  • Version 1.2: 2020-08-12
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Refinement description