3ZEI

Structure of the Mycobacterium tuberculosis O-Acetylserine Sulfhydrylase (OASS) CysK1 in complex with a small molecule inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Guided Design of Novel Thiazolidine Inhibitors of O-Acetyl Serine Sulfhydrylase from Mycobacterium Tuberculosis.

Poyraz, O.Jeankumar, V.U.Saxena, S.Schnell, R.Haraldsson, M.Yogeeswari, P.Sriram, D.Schneider, G.

(2013) J Med Chem 56: 6457

  • DOI: 10.1021/jm400710k
  • Primary Citation of Related Structures:  
    3ZEI

  • PubMed Abstract: 
  • The cysteine biosynthetic pathway is absent in humans but essential in microbial pathogens, suggesting that it provides potential targets for the development of novel antibacterial compounds. CysK1 is a pyridoxalphosphate-dependent O-acetyl sulfhydry ...

    The cysteine biosynthetic pathway is absent in humans but essential in microbial pathogens, suggesting that it provides potential targets for the development of novel antibacterial compounds. CysK1 is a pyridoxalphosphate-dependent O-acetyl sulfhydrylase, which catalyzes the formation of l-cysteine from O-acetyl serine and hydrogen sulfide. Here we report nanomolar thiazolidine inhibitors of Mycobacterium tuberculosis CysK1 developed by rational inhibitor design. The thiazolidine compounds were discovered using the crystal structure of a CysK1-peptide inhibitor complex as template. Pharmacophore modeling and subsequent in vitro screening resulted in an initial hit compound 2 (IC50 of 103.8 nM), which was subsequently optimized by a combination of protein crystallography, modeling, and synthetic chemistry. Hit expansion of 2 by chemical synthesis led to improved thiazolidine inhibitors with an IC50 value of 19 nM for the best compound, a 150-fold higher potency than the natural peptide inhibitor (IC50 2.9 μM).


    Organizational Affiliation

    Division of Molecular Structural Biology, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-ACETYLSERINE SULFHYDRYLASEA310Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.47
Find proteins for P9WP55 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP55 
Go to UniProtKB:  P9WP55
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AWH
Query on AWH

Download CCD File 
A
3-[(Z)-[(5Z)-5-[[2-(2-hydroxy-2-oxoethyloxy)phenyl]methylidene]-3-methyl-4-oxidanylidene-1,3-thiazolidin-2-ylidene]amino]benzoic acid
C20 H16 N2 O6 S
ZRWLYRDALGQUID-PTWQKYQPSA-N
 Ligand Interaction
PLP
Query on PLP

Download CCD File 
A
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AWHIC50:  103   nM  BindingDB
AWHIC50:  103   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.82α = 90
b = 71.82β = 90
c = 179.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references