3O0G

Crystal Structure of Cdk5:p25 in complex with an ATP analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Defining Cdk5 ligand chemical space with small molecule inhibitors of Tau phosphorylation

Ahn, J.S.Radhakrishnan, M.L.Mapelli, M.Choi, S.Tidor, B.Cuny, G.D.Musacchio, A.Yeh, L.Kosik, S.K.

(2005) Chem Biol 12: 811-823

  • DOI: 10.1016/j.chembiol.2005.05.011
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cyclin-dependent kinase 5 (Cdk5) is widely viewed as a possible target for a wide variety of neurological disorders. One pathological role attributed to Cdk5 is the abnormal phosphorylation of tau that may lead to the neuronal inclusions known as neu ...

    Cyclin-dependent kinase 5 (Cdk5) is widely viewed as a possible target for a wide variety of neurological disorders. One pathological role attributed to Cdk5 is the abnormal phosphorylation of tau that may lead to the neuronal inclusions known as neurofibrillary tangles. A high through-put screen for inhibitors of Cdk5-mediated phosphorylation of tau resulted in three compounds with distinct mechanisms of action. One compound is competitive with ATP and has a high affinity for the Cdk5 ATP binding pocket. The second compound also competes with ATP, is noncompetitive with tau, and (uniquely among this class of inhibitors) displaces adjacent amino acid residues to make room for the nitrophenyl group. A third compound did not compete with ATP, but did compete with tau at low concentrations of tau. The SAR and charge optimization derived from cocrystals of the two ATP competitors along with cocrystals of three other ATP competitors map out the importance of filling and properly charging different regions of the ATP binding pocket. Taken together, this analysis shows how the structure of Cdk5 constrains the space of potential inhibitors and reveals a pocket unfilled in all of the structures. These leads could be a starting point for structure-based drug design of more potent and selective inhibitors.


    Organizational Affiliation

    Department of Neurology and Laboratory for Drug Discovery in Neurodegeneration, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division protein kinase 5A, B292Homo sapiensMutation(s): 1 
Gene Names: CDK5CDKN5
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.1 (UniProt)
Find proteins for Q00535 (Homo sapiens)
Explore Q00535 
Go to UniProtKB:  Q00535
NIH Common Fund Data Resources
PHAROS  Q00535
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclin-dependent kinase 5 activator 1D, E149Homo sapiensMutation(s): 0 
Gene Names: p25CDK5R1CDK5RNCK5A
Find proteins for Q15078 (Homo sapiens)
Explore Q15078 
Go to UniProtKB:  Q15078
NIH Common Fund Data Resources
PHAROS  Q15078
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3O0
Query on 3O0

Download CCD File 
B
{4-amino-2-[(4-chlorophenyl)amino]-1,3-thiazol-5-yl}(3-nitrophenyl)methanone
C16 H11 Cl N4 O3 S
YQRVBHMYUSGXHL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3O0IC50:  750   nM  BindingDB
3O0Ki :  600   nM  PDBBind
3O0IC50:  2000   nM  Binding MOAD
3O0IC50:  2000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.124α = 90
b = 117.124β = 90
c = 155.599γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-07-19 
  • Released Date: 2011-01-26 
  • Deposition Author(s): Mapelli, M.

Revision History 

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description