3F5X

CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: Design and synthesis of a potent and isoform selective PKC-zeta inhibitor.

Trujillo, J.I., Kiefer, J.R., Huang, W., Thorarensen, A., Xing, L., Caspers, N.L., Day, J.E., Mathis, K.J., Kretzmer, K.K., Reitz, B.A., Weinberg, R.A., Stegeman, R.A., Wrightstone, A., Christine, L., Compton, R., Li, X.

(2009) Bioorg Med Chem Lett 19: 908-911

  • DOI: 10.1016/j.bmcl.2008.11.105
  • Primary Citation of Related Structures:  
    3EZR, 3EZV, 3F5X

  • PubMed Abstract: 

    • The inhibition of PKC-zeta has been proposed to be a potential drug target for immune and inflammatory diseases. A series of 2-(6-phenyl-1H indazol-3-yl)-1H-benzo[d]imidazoles with initial high crossover to CDK-2 has been optimized to afford potent and selective inhibitors of protein kinase c-zeta (PKC-zeta) ...

    The inhibition of PKC-zeta has been proposed to be a potential drug target for immune and inflammatory diseases. A series of 2-(6-phenyl-1H indazol-3-yl)-1H-benzo[d]imidazoles with initial high crossover to CDK-2 has been optimized to afford potent and selective inhibitors of protein kinase c-zeta (PKC-zeta). The determination of the crystal structures of key inhibitor:CDK-2 complexes informed the design and analysis of the series. The most selective and potent analog was identified by variation of the aryl substituent at the 6-position of the indazole template to give a 4-NH(2) derivative. The analog displays good selectivity over other PKC isoforms (alpha, betaII, gamma, delta, epsilon, mu, theta, eta and iota/lambda) and CDK-2, however it displays marginal selectivity against a panel of other kinases (37 profiled).

    Organizational Affiliation: 

    Department of Medicinal Chemistry, Pfizer Global Research and Development, 700 Chesterfield Pkwy, AA236, Chesterfield, MO 63017, USA. john.i.trujillo@pfizer.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division protein kinase 2A, C298Homo sapiensMutation(s): 0 
Gene Names: CDK2, CDKN2
EC: 2.7.11.22
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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-A2B, D256Homo sapiensMutation(s): 0 
Gene Names: CCNA2, CCN1, CCNA
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EZV
Query on EZV
Download Ideal Coordinates CCD File 
F [auth A],
H [auth C]		4-{3-[7-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-indazol-6-yl}aniline
C25 H25 N7
LPSCCOBGZSKECZ-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
E [auth A],
G [auth C]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EZV Binding MOAD:  3F5X IC50: 1040 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 62 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.051α = 90
b = 184.051β = 90
c = 214.848γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

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: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance