4AU8

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

• PDB DOI: https://doi.org/10.2210/pdb4AU8/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-05-14 Released: 2013-03-27 
• Deposition Author(s): 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.

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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 

Starting Model: other

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

• PubMed: 22889803 
• DOI: https://doi.org/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.

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Organizational Affiliation: 

Medicinal Chemistry, CNSP iMed Science, AstraZeneca R&D, Innovative Medicines, SE-15185 Södertälje, Sweden. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.48 kDa 
• Atom Count: 4,994 
• Modelled Residue Count: 553 
• Deposited Residue Count: 592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE 5	A, B	296	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Z3R	F [auth A], J [auth B]	4-(1,3-benzothiazol-2-yl)thiophene-2-sulfonamide C11 H8 N2 O2 S3 GKGZVFYMXSXLJJ-UHFFFAOYSA-N
SO4	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
IMD	K [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Binding Affinity Annotations
ID	Source	Binding Affinity
Z3R	BindingDB:  4AU8	IC50: 551 (nM) from 1 assay(s)
	PDBBind:  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 = 83.271	α = 90
b = 83.271	β = 90
c = 191.766	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description