2BKZ

STRUCTURE OF CDK2-CYCLIN A WITH PHA-404611


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Benzodipyrazoles: A New Class of Potent Cdk2 Inhibitors

Dalessio, R.Bargiottia, A.Metz, S.Brasca, M.G.Cameron, A.Ermoli, A.Marsiglio, A.Polucci, P.Roletto, F.Tibolla, M.Vazquez, M.L.Vulpetti, A.Pevarello, P.

(2005) Bioorg Med Chem Lett 15: 1315

  • DOI: 10.1016/j.bmcl.2005.01.023
  • Primary Citation of Related Structures:  
    2BKZ

  • PubMed Abstract: 
  • The synthesis and the preliminary expansion of this new class of CDK2 inhibitors are presented. The synthesis was accomplished using a solution-phase protocol amenable to rapid parallel expansion and suitable to be scaled-up in view of possible lead development ...

    The synthesis and the preliminary expansion of this new class of CDK2 inhibitors are presented. The synthesis was accomplished using a solution-phase protocol amenable to rapid parallel expansion and suitable to be scaled-up in view of possible lead development. Following a medicinal chemistry program aimed at improving cell permeability and selectivity, a series of compounds with nanomolar activity in the biochemical assay and able to efficiently inhibit tumor cell proliferation has been obtained.


    Organizational Affiliation

    Chemistry Department, Nerviano Medical Sciences, Oncology Business Unit, Viale Pasteur 10, 20014 Nerviano (MI), Italy. roberto.dalessio@nervianoms.com



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A, C309Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24941
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN A2B, D265Homo sapiensMutation(s): 0 
Gene Names: CCNA2CCN1CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
PHAROS:  P20248
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20248
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SBC
Query on SBC

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]
1-[4-(AMINOSULFONYL)PHENYL]-1,6-DIHYDROPYRAZOLO[3,4-E]INDAZOLE-3-CARBOXAMIDE
C15 H12 N6 O3 S
HGAKLLFPOGATII-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SBC PDBBind:  2BKZ IC50: 7 (nM) from 1 assay(s)
BindingDB:  2BKZ IC50: 0.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.230 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.862α = 90
b = 183.862β = 90
c = 214.572γ = 120
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-08
    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