1UNH

Structural mechanism for the inhibition of CDK5-p25 by roscovitine, aloisine and indirubin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of Cdk5/P25 Binding by Cdk Inhibitors

Mapelli, M.Massimilinao, L.Crovace, C.Seeliger, M.A.Tsai, L.-H.Meijer, L.Musacchio, A.

(2005) J.Med.Chem. 48: 671

  • DOI: 10.1021/jm049323m
  • Primary Citation of Related Structures:  1UNG, 1UNL

  • PubMed Abstract: 
  • The cyclin-dependent kinases (CDK) CDK1, CDK2, CDK4, and CDK6 are serine/threonine protein kinases targeted in cancer therapy due to their role in cell cycle progression. The postmitotic CDK5 is involved in biological pathways important for neuronal ...

    The cyclin-dependent kinases (CDK) CDK1, CDK2, CDK4, and CDK6 are serine/threonine protein kinases targeted in cancer therapy due to their role in cell cycle progression. The postmitotic CDK5 is involved in biological pathways important for neuronal migration and differentiation. CDK5 represents an attractive pharmacological target as its deregulation is implicated in various neurodegenerative diseases such as Alzheimer's, Parkinson's, and Niemann-Pick type C diseases, ischemia, and amyotrophic lateral sclerosis. We have generated an improved crystal form of CDK5 in complex with p25, a segment of the p35 neuronal activator. The crystals were used to solve the structure of CDK5/p25 with (R)-roscovitine and aloisine at a resolution of 2.2 and 2.3 A, respectively. The structure of CDK5/p25/roscovitine provides a rationale for the preference of CDK5 for the R over the S stereoisomer. Furthermore, roscovitine stabilized an unusual collapsed conformation of the glycine-rich loop, an important site of CDK regulation, and we report an investigation of the effects of glycine-rich loop phosphorylation on roscovitine binding. The CDK5/p25 crystals represent a valuable new tool for the identification and optimization of selective CDK inhibitors.


    Organizational Affiliation

    Structural Biology Unit, Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 5
A, B
292Homo sapiensGene Names: CDK5 (CDKN5)
EC: 2.7.11.1
Find proteins for Q00535 (Homo sapiens)
Go to Gene View: CDK5
Go to UniProtKB:  Q00535
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 5 ACTIVATOR 1
D, E
208Homo sapiensGene Names: CDK5R1 (CDK5R, NCK5A)
Find proteins for Q15078 (Homo sapiens)
Go to Gene View: CDK5R1
Go to UniProtKB:  Q15078
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IXM
Query on IXM

Download SDF File 
Download CCD File 
A, B
(Z)-1H,1'H-[2,3']BIINDOLYLIDENE-3,2'-DIONE-3-OXIME
INDIRUBIN-3'-MONOXIME
C16 H11 N3 O2
HBDSHCUSXQATPO-BGBJRWHRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IXMIC50: 100 nM BINDINGMOAD
IXMIC50: 100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 149.541α = 90.00
b = 90.124β = 93.29
c = 83.158γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance