3F9N | pdb_00003f9n

Crystal structure of chk1 kinase in complex with inhibitor 38

• PDB DOI: https://doi.org/10.2210/pdb3F9N/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-11-14 Released: 2009-01-20 
• Deposition Author(s): Yan, Y., Munshi, S., Ikuta, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.216 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Development of thioquinazolinones, allosteric Chk1 kinase inhibitors.

Converso, A., Hartingh, T., Garbaccio, R.M., Tasber, E., Rickert, K., Fraley, M.E., Yan, Y., Kreatsoulas, C., Stirdivant, S., Drakas, B., Walsh, E.S., Hamilton, K., Buser, C.A., Mao, X., Abrams, M.T., Beck, S.C., Tao, W., Lobell, R., Sepp-Lorenzino, L., Zugay-Murphy, J., Sardana, V., Munshi, S.K., Jezequel-Sur, S.M., Zuck, P.D., Hartman, G.D.

(2009) Bioorg Med Chem Lett 19: 1240-1244

• PubMed: 19155174 
• DOI: https://doi.org/10.1016/j.bmcl.2008.12.076
• Primary Citation Related Structures: 
  3F9N


• PubMed Abstract: 
  

  A high throughput screening campaign was designed to identify allosteric inhibitors of Chk1 kinase by testing compounds at high concentration. Activity was then observed at K(m) for ATP and at near-physiological concentrations of ATP. This strategy led to the discovery of a non-ATP competitive thioquinazolinone series which was optimized for potency and stability. An X-ray crystal structure for the complex of our best inhibitor bound to Chk1 was solved, indicating that it binds to an allosteric site approximately 13A from the ATP binding site. Preliminary data is presented for several of these compounds.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Merck Research Laboratories, Merck & Co., PO Box 4, West Point, PA 19486, 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: 37.52 kDa 
• Atom Count: 2,375 
• Modeled Residue Count: 253 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	322	Homo sapiens	Mutation(s): 0  Gene Names: CHEK1, CHK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14757 (Homo sapiens) Explore O14757  Go to UniProtKB:  O14757
PHAROS:  O14757 GTEx:  ENSG00000149554

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
38M	B [auth A]	3-(3-chlorophenyl)-2-({(1S)-1-[(6S)-2,8-diazaspiro[5.5]undec-2-ylcarbonyl]pentyl}sulfanyl)quinazolin-4(3H)-one C29 H35 Cl N4 O2 S GMBUMIBZLYNLLU-SVEHJYQDSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.216 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.06	α = 90
b = 65.75	β = 96.24
c = 58.41	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
BUSTER-TNT	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER-TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-20 
Deposition Author(s): Yan, Y., Munshi, S., Ikuta, M.

Revision History  

• Version 1.0: 2009-01-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description