2C5X

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
  • Also Cited By: 2UUE, 2V22

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CELL DIVISION PROTEIN KINASE 2
A, C
298Homo sapiensMutation(s): 0 
Gene Names: CDK2 (CDKN2)
EC: 2.7.11.22
Find proteins for P24941 (Homo sapiens)
Go to Gene View: CDK2
Go to UniProtKB:  P24941
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN A2
B, D
259Homo sapiensMutation(s): 0 
Gene Names: CCNA2 (CCN1, CCNA)
Find proteins for P20248 (Homo sapiens)
Go to Gene View: CCNA2
Go to UniProtKB:  P20248
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTW
Query on MTW
Download SDF File 
Download CCD File 
A, C
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MTWIC50: 250 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.334α = 90.00
b = 112.352β = 90.00
c = 154.911γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-04-03
    Type: Data collection, Other, Source and taxonomy