Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 
    0.280 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.238 (Depositor), 0.238 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1VYZ

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

3-Aminopyrazole Inhibitors of Cdk2/Cyclin a as Antitumor Agents. 1. Lead Finding

Pevarello, P.Brasca, M.G.Amici, R.Orsini, P.Traquandi, G.Corti, L.Piutti, C.Sansonna, P.Villa, M.Pierce, B.S.Pulici, M.Giordano, P.Martina, K.Fritzen, E.Nugent, R.A.Casale, E.Cameron, A.Ciomei, M.Roletto, F.Isacchi, A.Fogliatto, G.Pesenti, E.Pastori, W.Marsiglio, A.Leach, K.L.Clare, P.M.Fiorentini, F.Varasi, M.Vulpetti, A.Warpehoski, M.A.

(2004) J Med Chem 47: 3367

  • DOI: https://doi.org/10.1021/jm031145u
  • Primary Citation Related Structures: 
    1VYW, 1VYZ

  • PubMed Abstract: 

    Abnormal proliferation mediated by disruption of the normal cell cycle mechanisms is a hallmark of virtually all cancer cells. Compounds targeting complexes between cyclin-dependent kinases (CDK) and cyclins, such as CDK2/cyclin A and CDK2/cyclin E, and inhibiting their kinase activity are regarded as promising antitumor agents to complement the existing therapies. From a high-throughput screening effort, we identified a new class of CDK2/cyclin A/E inhibitors. The hit-to-lead expansion of this class is described. X-ray crystallographic data of early compounds in this series, as well as in vitro testing funneled for rapidly achieving in vivo efficacy, led to a nanomolar inhibitor of CDK2/cyclin A (N-(5-cyclopropyl-1H-pyrazol-3-yl)-2-(2-naphthyl)acetamide (41), PNU-292137, IC50 = 37 nM) with in vivo antitumor activity (TGI > 50%) in a mouse xenograft model at a dose devoid of toxic effects.


  • Organizational Affiliation
    • Chemistry Department, Pharmacia Italia, Viale Pasteur 10, 20014 Nerviano (MI), Italy. paolo.pevarello@pharmacia.com

Macromolecule Content 

  • Total Structure Weight: 34.2 kDa 
  • Atom Count: 2,326 
  • Modeled Residue Count: 279 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2298Homo sapiensMutation(s): 0 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
PHAROS:  P24941
GTEx:  ENSG00000123374 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N5B

Query on N5B



Download:Ideal Coordinates CCD File
B [auth A]N-(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)BENZAMIDE
C13 H13 N3 O
LUCORKWTQSQFFU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free:  0.280 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.238 (Depositor), 0.238 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.25α = 90
b = 71.91β = 90
c = 72.22γ = 90
Software Package:
Software NamePurpose
CNXrefinement
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-04-03
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other