3PA5 | pdb_00003pa5

X-ray crystal structure of compound 1 bound to human CHK1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3PA5/pdb

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


• Deposited: 2010-10-18 Released: 2010-12-08 
• Deposition Author(s): Fischmann, T.O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.204 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 

Literature

Design, synthesis and SAR of thienopyridines as potent CHK1 inhibitors.

Zhao, L., Zhang, Y., Dai, C., Guzi, T., Wiswell, D., Seghezzi, W., Parry, D., Fischmann, T., Siddiqui, M.A.

(2010) Bioorg Med Chem Lett 20: 7216-7221

• PubMed: 21074424 
• DOI: https://doi.org/10.1016/j.bmcl.2010.10.105
• Primary Citation of Related Structures:  
  3PA3, 3PA4, 3PA5


• PubMed Abstract: 
  

  A novel series of CHK1 inhibitors based on thienopyridine template has been designed and synthesized. These inhibitors maintain critical hydrogen bonding with the hinge and conserved water in the ATP binding site. Several compounds show single digit nanomolar CHK1 activities. Compound 70 shows excellent enzymatic activity of 1 nM.

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Organizational Affiliation: 

Department of Chemistry, Merck Research Laboratories, Cambridge, MA 02141, 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: 32.11 kDa 
• Atom Count: 2,323 
• Modeled Residue Count: 257 
• Deposited Residue Count: 273 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	273	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
C73	B [auth A]	2-(carbamoylamino)-5-(4-chlorophenyl)-N-[(3S)-piperidin-3-yl]thiophene-3-carboxamide C17 H19 Cl N4 O2 S MZBVMTJFZZINAF-LBPRGKRZSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
C73	BindingDB:  3PA5	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.204 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.84	α = 90
b = 65.85	β = 94.68
c = 58.25	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Fischmann, T.O.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations