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 evolutionary related protease adenain a target-hopping approach screening on a focused set of adenain inhibitors has been pursue ...

    Based on the similarity between the active sites of the deubiquitylating and deneddylating enzyme ChlaDub1 (Cdu1) and the evolutionary related protease adenain a target-hopping approach screening on a focused set of adenain inhibitors has been pursued. The thereby identified cyano-pyrimidine based inhibitors represent the first active-site directed small molecule inhibitors for Cdu1. High-resolution crystal structures of Cdu1 in complex with two covalently bound cyano-pyrimidines as well as with its substrate ubiquitin have been obtained. These structural data were complemented by enzymatic assays and covalent docking studies to provide insight into Cdu1s substrate recognition, active site pocket flexibility and potential hotspots for ligand interaction. Combined, these data provide a strong foundation for future structure-guided medicinal chemistry optimization of this cyano-pyrimidine based scaffold towards more potent and specific Cdu1 inhibitors.


    Organizational Affiliation

    University of Wuerzburg, Structural Biology, Josef-Schneider-Stra├če 2, 97080, Germany, 97080, Wuerzburg, GERMANY.




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
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement

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