2GDO

4-(Aminoalkylamino)-3-Benzimidazole-Quinolinones As Potent CHK1 Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb2GDO/pdb

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


• Deposited: 2006-03-16 Released: 2007-03-20 
• Deposition Author(s): Le, V., Dove, J., Fang, E., Bussiere, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

4-(Aminoalkylamino)-3-benzimidazole-quinolinones as potent CHK-1 inhibitors.

Ni, Z.J., Barsanti, P., Brammeier, N., Diebes, A., Poon, D.J., Ng, S., Pecchi, S., Pfister, K., Renhowe, P.A., Ramurthy, S., Wagman, A.S., Bussiere, D.E., Le, V., Zhou, Y., Jansen, J.M., Ma, S., Gesner, T.G.

(2006) Bioorg Med Chem Lett 16: 3121-3124

• PubMed: 16603354 
• DOI: https://doi.org/10.1016/j.bmcl.2006.03.059
• Primary Citation of Related Structures:  
  2GDO


• PubMed Abstract: 
  

  CHK-1 is one of the key enzymes regulating checkpoints in cellular growth cycles. Novel 4-(amino-alkylamino)-3-benzimidazole-quinolinones were prepared and assayed for their ability to inhibit CHK-1. These compounds are potent cell permeable CHK-1 inhibitors and showed synergistic effect with a DNA-damaging agent, camptothecin.

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Organizational Affiliation: 

Chiron Corporation, 4560 Horton Street, Emeryville, CA 94608, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.48 kDa 
• Atom Count: 2,399 
• Modelled Residue Count: 269 
• Deposited Residue Count: 295 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase Chk1	A	295	Homo sapiens	Mutation(s): 0  Gene Names: CHK1 EC: 2.7.1.37
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
12C	D [auth A]	4-[(3S)-1-AZABICYCLO[2.2.2]OCT-3-YLAMINO]-3-(1H-BENZIMIDAZOL-2-YL)-6-CHLOROQUINOLIN-2(1H)-ONE C23 H22 Cl N5 O MOVBBVMDHIRCTG-LJQANCHMSA-N
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
12C	BindingDB:  2GDO	IC50: min: 0.3, max: 0.32 (nM) from 2 assay(s)
	PDBBind:  2GDO	IC50: 0.32 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.259 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.704	α = 90
b = 65.337	β = 93.95
c = 57.517	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
CrystalClear	data reduction
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Le, V., Dove, J., Fang, E., Bussiere, D.E.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations