4AU8

Crystal structure of compound 4a in complex with cdk5, showing an unusual binding mode to the hinge region via a water molecule


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Synthesis and Structure-Activity Relationship of 4-(1,3-Benzothiazol-2-Yl)-Thiophene-2-Sulfonamides as Cyclin-Dependent Kinase 5 (Cdk5)/P25 Inhibitors.

Malmstrom, J.Viklund, J.Slivo, C.Costa, A.Maudet, M.Sandelin, C.Hiller, G.Olsson, L.L.Aagaard, A.Geschwindner, S.Xue, Y.Vasange, M.

(2012) Bioorg.Med.Chem.Lett. 22: 5919

  • DOI: 10.1016/j.bmcl.2012.07.068

  • PubMed Abstract: 
  • 4-(1,3-Benzothiazol-2-yl)thiophene-2-sulfonamide (4a) was found to be a moderately potent inhibitor of cyclin-dependent kinase 5 (cdk5) from a HTS screen. The synthesis and SAR around this hit is described. The X-ray coordinates of ligand 4a with cdk ...

    4-(1,3-Benzothiazol-2-yl)thiophene-2-sulfonamide (4a) was found to be a moderately potent inhibitor of cyclin-dependent kinase 5 (cdk5) from a HTS screen. The synthesis and SAR around this hit is described. The X-ray coordinates of ligand 4a with cdk5 are also reported, showing an unusual binding mode to the hinge region via a water molecule.


    Organizational Affiliation

    Medicinal Chemistry, CNSP iMed Science, AstraZeneca R&D, Innovative Medicines, SE-15185 Södertälje, Sweden. Jonas.Malmstrom@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLIN-DEPENDENT KINASE 5
A, B
296Homo sapiensMutation(s): 0 
Gene Names: CDK5 (CDKN5)
EC: 2.7.11.1
Find proteins for Q00535 (Homo sapiens)
Go to Gene View: CDK5
Go to UniProtKB:  Q00535
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Z3R
Query on Z3R

Download SDF File 
Download CCD File 
A, B
4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide
C11 H8 N2 O2 S3
GKGZVFYMXSXLJJ-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Z3RIC50: 551 nM BINDINGMOAD
Z3RIC50: 551 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 83.271α = 90.00
b = 83.271β = 90.00
c = 191.766γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release