2C5V

Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug Design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


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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:  
    2C5Y, 2C5X, 2C5V, 2C5O, 2C5N

  • 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 ...

    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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN A2BD259Homo sapiensMutation(s): 0 
Gene Names: CCNA2CCN1CCNA
Find proteins for P20248 (Homo sapiens)
Explore P20248 
Go to UniProtKB:  P20248
NIH Common Fund Data Resources
PHAROS  P20248
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN KINASE 2AC298Homo sapiensMutation(s): 0 
Gene Names: CDK2CDKN2
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.22 (UniProt)
Find proteins for P24941 (Homo sapiens)
Explore P24941 
Go to UniProtKB:  P24941
NIH Common Fund Data Resources
PHAROS  P24941
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ALA-ALA-ABA-ARG-SER-LEU-ILE-PFF-NH2FH9synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CK4
Query on CK4

Download CCD File 
A, C
4-(2,4-DIMETHYL-1,3-THIAZOL-5-YL)-N-[4-(TRIFLUOROMETHYL)PHENYL]PYRIMIDIN-2-AMINE
C16 H13 F3 N4 S
MEZFDQUDLQCVNX-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ABA
Query on ABA
F,HL-PEPTIDE LINKINGC4 H9 N O2ALA
PFF
Query on PFF
F,HL-PEPTIDE LINKINGC9 H10 F N O2PHE
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CK4Ki:  290   nM  BindingDB
CK4IC50:  290   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.501α = 90
b = 114.549β = 90
c = 156.994γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-01
    Type: Initial release
  • Version 1.1: 2017-02-08
    Changes: Derived calculations, Non-polymer description, Other, Source and taxonomy, Version format compliance