2C5Y

DIFFERENTIAL BINDING OF INHIBITORS TO ACTIVE AND INACTIVE CDK2 PROVIDES INSIGHTS FOR DRUG DESIGN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design.

Kontopidis, G.Mcinnes, C.Pandalaneni, S.R.Mcnae, I.Gibson, D.Mezna, M.Thomas, M.Wood, G.Wang, S.Walkinshaw, M.D.Fischer, P.M.

(2006) Chem Biol 13: 201

  • DOI: 10.1016/j.chembiol.2005.11.011
  • Primary Citation of Related Structures:  
    2C5N, 2C5O, 2C5V, 2C5X, 2C5Y

  • PubMed Abstract: 
  • The cyclin-dependent kinases (CDKs) have been characterized in complex with a variety of inhibitors, but the majority of structures solved are in the inactive form. We have solved the structures of six inhibitors in both the monomeric CDK2 and binary CDK2/cyclinA complexes and demonstrate that significant differences in ligand binding occur depending on the activation state ...

    The cyclin-dependent kinases (CDKs) have been characterized in complex with a variety of inhibitors, but the majority of structures solved are in the inactive form. We have solved the structures of six inhibitors in both the monomeric CDK2 and binary CDK2/cyclinA complexes and demonstrate that significant differences in ligand binding occur depending on the activation state. The binding mode of two ligands in particular varies substantially in active and inactive CDK2. Furthermore, energetic analysis of CDK2/cyclin/inhibitors demonstrates that a good correlation exists between the in vitro potency and the calculated energies of interaction, but no such relationship exists for CDK2/inhibitor structures. These results confirm that monomeric CDK2 ligand complexes do not fully reflect active conformations, revealing significant implications for inhibitor design while also suggesting that the monomeric CDK2 conformation can be selectively inhibited.


    Organizational Affiliation

    Cyclacel Ltd., Dundee, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2A298Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTW (Subject of Investigation/LOI)
Query on MTW

Download Ideal Coordinates CCD File 
B [auth A]HYDROXY(OXO)(3-{[(2Z)-4-[3-(1H-1,2,4-TRIAZOL-1-YLMETHYL)PHENYL]PYRIMIDIN-2(5H)-YLIDENE]AMINO}PHENYL)AMMONIUM
C19 H15 N7 O2
PLQVWKCQWFFUFJ-NMWGTECJSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MTW Binding MOAD:  2C5Y IC50: 250 (nM) from 1 assay(s)
PDBBind:  2C5Y IC50: 250 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.274α = 90
b = 70.893β = 90
c = 71.745γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata 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: 2006-03-01
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references, Derived calculations, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation, Other