6FDK

Structure of Chlamydia trachomatis effector protein Cdu1 bound to ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis.

Ramirez, Y.A.Adler, T.B.Altmann, E.Klemm, T.Tiesmeyer, C.Sauer, F.Kathman, S.G.Statsyuk, A.V.Sotriffer, C.Kisker, C.

(2018) ChemMedChem 13: 2014-2023

  • DOI: 10.1002/cmdc.201800364
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Based on the similarity between the active sites of the deubiquitylating and deneddylating enzyme ChlaDub1 (Cdu1) and the evolutionarily related protease adenain, a target-hopping screening approach on a focused set of adenain inhibitors was investig ...

    Based on the similarity between the active sites of the deubiquitylating and deneddylating enzyme ChlaDub1 (Cdu1) and the evolutionarily related protease adenain, a target-hopping screening approach on a focused set of adenain inhibitors was investigated. The cyanopyrimidine-based inhibitors identified represent the first active-site-directed small-molecule inhibitors of Cdu1. High-resolution crystal structures of Cdu1 in complex with two covalently bound cyanopyrimidines, as well as with its substrate ubiquitin, were obtained. These structural data were complemented by enzymatic assays and covalent docking studies to provide insight into the substrate recognition of Cdu1, active-site pocket flexibility and potential hotspots for ligand interaction. Combined, these data provide a strong basis for future structure-guided medicinal chemistry optimization of this cyanopyrimidine scaffold into more potent and selective Cdu1 inhibitors.


    Organizational Affiliation

    University of Houston, College of Pharmacy, 4849 Calhoun Road, Houston, 77204, TX, USA.,Novartis Institute for Biomedical Research, Novartis Campus, 4002, Basel, Switzerland.,Rudolf Virchow Center for Experimental Biomedicine, Institute of Structural Biology, University of Würzburg, Josef-Schneider-Straße 2, 97080, Würzburg, Germany.,Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.,Northwestern University, Department of Chemistry, Silverman Hall, Sheridan Road 2145, Evanston, 60208, IL, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deubiquitinase and deneddylase Dub1
A
266Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B)Mutation(s): 3 
Gene Names: cdu1
EC: 3.4.22.-
Find proteins for B0B9A0 (Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B))
Go to UniProtKB:  B0B9A0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AYE
Query on AYE

Download SDF File 
Download CCD File 
B
prop-2-en-1-amine
ALLYLAMINE
C3 H7 N
VVJKKWFAADXIJK-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AYE
Query on AYE
B
NON-POLYMERC3 H7 N

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.815α = 90.00
b = 56.937β = 104.86
c = 60.695γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GSLS University of WuerzburgGermany--

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references