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: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    4AU8

  • 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 cdk5 are also reported, showing an unusual binding mode to the hinge region via a water molecule ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE 5A, B296Homo sapiensMutation(s): 0 
Gene Names: CDK5CDKN5
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q00535 (Homo sapiens)
Explore Q00535 
Go to UniProtKB:  Q00535
PHAROS:  Q00535
GTEx:  ENSG00000164885 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00535
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Z3R
Query on Z3R

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide
C11 H8 N2 O2 S3
GKGZVFYMXSXLJJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IMD
Query on IMD

Download Ideal Coordinates CCD File 
K [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
Z3R Binding MOAD:  4AU8 IC50: 551 (nM) from 1 assay(s)
PDBBind:  4AU8 IC50: 551 (nM) from 1 assay(s)
BindingDB:  4AU8 IC50: 551 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.271α = 90
b = 83.271β = 90
c = 191.766γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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