4ANM

Complex of CK2 with a CDC7 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2012.04.024

  • 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 thi ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CASEIN KINASE II SUBUNIT ALPHA
A
335Zea maysMutation(s): 0 
Gene Names: ACK2
EC: 2.7.11.1
Find proteins for P28523 (Zea mays)
Go to UniProtKB:  P28523
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WUL
Query on WUL

Download SDF File 
Download CCD File 
A
8-BROMANYL-2-[[(3S)-3-OXIDANYLPYRROLIDIN-1-YL]METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE
(S)-8-BROMO-2-((3-HYDROXYPYRROLIDIN-1-YL)METHYL)
C15 H14 Br N3 O3
FRRLLRQAGKSVMU-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WULIC50: 28 nM BINDINGMOAD
WULIC50: 28 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 142.061α = 90.00
b = 60.549β = 102.92
c = 44.747γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-20 
  • Released Date: 2012-05-23 
  • Deposition Author(s): Stout, T.J.

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release