3NLB

Novel kinase profile highlights the temporal basis of context dependent checkpoint pathways to cell death

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Context-dependent cell cycle checkpoint abrogation by a novel kinase inhibitor

Massey, A.J., Borgognoni, J., Bentley, C., Foloppe, N., Fiumana, A., Walmsley, L.

(2010) PLoS One 5: e13123-e13123

  • DOI: https://doi.org/10.1371/journal.pone.0013123
  • Primary Citation of Related Structures:  
    3NLB

  • PubMed Abstract: 

    Checkpoint kinase 1 and 2 (Chk1/Chk2), and the Aurora kinases play a critical role in the activation of the DNA damage response and mitotic spindle checkpoints. We have identified a novel inhibitor of these kinases and utilized this molecule to probe the functional interplay between these two checkpoints.

    • Organizational Affiliation: 

    Vernalis R&D Ltd, Granta Park, Cambridge, United Kingdom. a.massey@vernalis.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase Chk1297Homo sapiensMutation(s): 0 
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14757
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5BE
Query on 5BE
Download Ideal Coordinates CCD File 
B [auth A]3-methyl-5-[5-(1-methylethyl)-1H-benzimidazol-2-yl]-N-(1-methylpiperidin-4-yl)-1H-pyrazole-4-carboxamide
C21 H28 N6 O
PFGGMNGDLVJXNC-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
5BE PDBBind:  3NLB IC50: 35 (nM) from 1 assay(s)
Binding MOAD:  3NLB IC50: 35 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.885α = 90
b = 65.71β = 102.7
c = 54.42γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations