Complex of CK2 with a CDC7 inhibitor

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: other
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This is version 1.1 of the entry. See complete history


Discovery of Xl413, a Potent and Selective Cdc7 Inhibitor.

Koltun, E.S.Tsuhako, A.L.Brown, D.S.Aay, N.Arcalas, A.Chan, V.Du, H.Engst, S.Ferguson, K.Franzini, M.Galan, A.Holst, C.R.Huang, P.Kane, B.Kim, M.H.Li, J.Markby, D.Mohan, M.Noson, K.Plonowski, A.Richards, S.J.Robertson, S.Shaw, K.Stott, G.Stout, T.J.Young, J.Yu, P.Zaharia, C.A.Zhang, W.Zhou, P.Nuss, J.M.Xu, W.Kearney, P.C.

(2012) Bioorg Med Chem Lett 22: 3727

  • DOI: https://doi.org/10.1016/j.bmcl.2012.04.024
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    CDC7 is a serine/threonine kinase that has been shown to be required for the initiation and maintenance of DNA replication. Up-regulation of CDC7 is detected in multiple tumor cell lines, with inhibition of CDC7 resulting in cell cycle arrest. In this paper, we disclose the discovery of a potent and selective CDC7 inhibitor, XL413 (14), which was advanced into Phase 1 clinical trials. Starting from advanced lead 3, described in a preceding communication, we optimized the CDC7 potency and selectivity to demonstrate in vitro CDC7 dependent cell cycle arrest and in vivo tumor growth inhibition in a Colo-205 xenograft model.

  • Organizational Affiliation

    Exelixis, Department of Drug Discovery, South San Francisco, CA 94080, USA. elena@numerate.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CASEIN KINASE II SUBUNIT ALPHA335Zea maysMutation(s): 0 
Find proteins for P28523 (Zea mays)
Explore P28523 
Go to UniProtKB:  P28523
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28523
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on WUL

Download Ideal Coordinates CCD File 
C15 H14 Br N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
WUL PDBBind:  4ANM IC50: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.061α = 90
b = 60.549β = 102.92
c = 44.747γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2012-05-23 
  • Deposition Author(s): Stout, T.J.

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description