4ANM

Complex of CK2 with a CDC7 inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ANM/pdb

• Classification: TRANSFERASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.202 
• R-Value Work: 0.164 
• R-Value Observed: 0.166 

Starting Model: other

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

• PubMed: 22560567 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.024
• Primary Citation of Related Structures:  
  4ANM


• 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.

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Organizational Affiliation: 

Exelixis, Department of Drug Discovery, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39.94 kDa 
• Atom Count: 3,125 
• Modelled Residue Count: 328 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CASEIN KINASE II SUBUNIT ALPHA	A	335	Zea mays	Mutation(s): 0  EC: 2.7.11.1
UniProt
Find proteins for P28523 (Zea mays) Explore P28523  Go to UniProtKB:  P28523

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WUL	B [auth A]	8-BROMANYL-2-[[(3S)-3-OXIDANYLPYRROLIDIN-1-YL]METHYL]-3H-[1]BENZOFURO[3,2-D]PYRIMIDIN-4-ONE C15 H14 Br N3 O3 FRRLLRQAGKSVMU-VIFPVBQESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
WUL	PDBBind:  4ANM	IC50: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 142.061	α = 90
b = 60.549	β = 102.92
c = 44.747	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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