3TKI

Crystal structure of Chk1 in complex with inhibitor S25

• PDB DOI: https://doi.org/10.2210/pdb3TKI/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2011-08-26 Released: 2012-04-11 
• Deposition Author(s): Yan, Y., Ikuta, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Pyridyl aminothiazoles as potent inhibitors of Chk1 with slow dissociation rates.

Dudkin, V.Y., Rickert, K., Kreatsoulas, C., Wang, C., Arrington, K.L., Fraley, M.E., Hartman, G.D., Yan, Y., Ikuta, M., Stirdivant, S.M., Drakas, R.A., Walsh, E.S., Hamilton, K., Buser, C.A., Lobell, R.B., Sepp-Lorenzino, L.

(2012) Bioorg Med Chem Lett 22: 2609-2612

• PubMed: 22374217 
• DOI: https://doi.org/10.1016/j.bmcl.2012.01.110
• Primary Citation of Related Structures:  
  3TKH, 3TKI


• PubMed Abstract: 
  

  Pyridyl aminothiazoles comprise a novel class of ATP-competitive Chk1 inhibitors with excellent inhibitory potential. Modification of the core with ethylenediamine amides provides compounds with low picomolar potency and very high residence times. Investigation of binding parameters of such compounds using X-ray crystallography and molecular dynamics simulations revealed multiple hydrogen bonds to the enzyme backbone as well as stabilization of the conserved water molecules network in the hydrophobic binding region.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, 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: 37.44 kDa 
• Atom Count: 2,433 
• Modelled Residue Count: 272 
• Deposited Residue Count: 323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	323	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
S25	C [auth A]	N-(2-aminoethyl)-5-(2-{[4-(morpholin-4-yl)pyridin-2-yl]amino}-1,3-thiazol-5-yl)pyridine-3-carboxamide C20 H23 N7 O2 S TWDABHIMTXVQHI-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
S25	BindingDB:  3TKI	IC50: 0.05 (nM) from 1 assay(s)
	PDBBind:  3TKI	IC50: 0.05 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.212 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45	α = 90
b = 65.24	β = 94.53
c = 57.91	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
BUSTER	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Yan, Y., Ikuta, M.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description