5A14

Human CDK2 with type II inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Type II Inhibitors Targeting Cdk2.

Alexander, L.T.Mobitz, H.Drueckes, P.Savitsky, P.Fedorov, O.Elkins, J.M.Deane, C.M.Cowan-Jacob, S.W.Knapp, S.

(2015) ACS Chem Biol 10: 2116

  • DOI: 10.1021/acschembio.5b00398
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We ...

    Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.


    Organizational Affiliation

    Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University , Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 2
A
299Homo sapiensMutation(s): 1 
Gene Names: CDK2CDKN2
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
Find proteins for P24941 (Homo sapiens)
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LQ5
Query on LQ5

Download CCD File 
A
1-[4-(2-azanylpyrimidin-4-yl)oxyphenyl]-3-[4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl]urea
C24 H26 F3 N7 O2
PWDLXPJQFNVTNL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LQ5-TΔS:  23.049999237060547   kJ/mol  BindingDB
LQ5ΔH:  76.0999984741211   kJ/mol  BindingDB
LQ5ΔH:  33.29999923706055   kJ/mol  BindingDB
LQ5-TΔS:  5.989999771118164   kJ/mol  BindingDB
LQ5ΔG:  40   kJ/mol  BindingDB
LQ5ΔG:  36.599998474121094   kJ/mol  BindingDB
LQ5ΔG:  44.400001525878906   kJ/mol  BindingDB
LQ5IC50:  800   nM  BindingDB
LQ5ΔG:  34.7599983215332   kJ/mol  BindingDB
LQ5Kd:  9.699999809265137   nM  BindingDB
LQ5ΔG:  30.299999237060547   kJ/mol  BindingDB
LQ5ΔG:  29.799999237060547   kJ/mol  BindingDB
LQ5-TΔS:  1683.699951171875   kJ/mol  BindingDB
LQ5ΔG:  27.299999237060547   kJ/mol  BindingDB
LQ5ΔH:  62.58000183105469   kJ/mol  BindingDB
LQ5ΔH:  36.70000076293945   kJ/mol  BindingDB
LQ5-TΔS:  21.899999618530273   kJ/mol  BindingDB
LQ5ΔG:  30.700000762939453   kJ/mol  BindingDB
LQ5-TΔS:  3.5799999237060547   kJ/mol  BindingDB
LQ5IC50:  10000   nM  BindingDB
LQ5IC50:  10000   nM  BindingDB
LQ5IC50:  7200   nM  BindingDB
LQ5Kd:  50   nM  BindingDB
LQ5ΔH:  15.600000381469727   kJ/mol  BindingDB
LQ5ΔG:  35.79999923706055   kJ/mol  BindingDB
LQ5ΔG:  42.70000076293945   kJ/mol  BindingDB
LQ5-TΔS:  39.34000015258789   kJ/mol  BindingDB
LQ5ΔH:  30.299999237060547   kJ/mol  BindingDB
LQ5Kd:  18.600000381469727   nM  BindingDB
LQ5Kd:  15.399999618530273   nM  BindingDB
LQ5-TΔS:  4.199999809265137   kJ/mol  BindingDB
LQ5ΔH:  66.1500015258789   kJ/mol  BindingDB
LQ5-TΔS:  61.09000015258789   kJ/mol  BindingDB
LQ5ΔH:  53.5099983215332   kJ/mol  BindingDB
LQ5ΔH:  42.75   kJ/mol  BindingDB
LQ5ΔG:  32.939998626708984   kJ/mol  BindingDB
LQ5ΔH:  74.0999984741211   kJ/mol  BindingDB
LQ5-TΔS:  6.849999904632568   kJ/mol  BindingDB
LQ5-TΔS:  2.619999885559082   kJ/mol  BindingDB
LQ5ΔH:  61.900001525878906   kJ/mol  BindingDB
LQ5ΔH:  31.5   kJ/mol  BindingDB
LQ5-TΔS:  19.8799991607666   kJ/mol  BindingDB
LQ5ΔG:  43.099998474121094   kJ/mol  BindingDB
LQ5-TΔS:  31.700000762939453   kJ/mol  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.41α = 90
b = 67.27β = 90
c = 89.13γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Database references, Derived calculations, Other