4YRK

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with (4-chlorophenyl)methanol (Chem 260)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


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Literature

A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens.

Koh, C.Y., Siddaramaiah, L.K., Ranade, R.M., Nguyen, J., Jian, T., Zhang, Z., Gillespie, J.R., Buckner, F.S., Verlinde, C.L., Fan, E., Hol, W.G.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1684-1698

  • DOI: 10.1107/S1399004715007683
  • Primary Citation of Related Structures:  
    4YP0, 4YPF, 4YRC, 4YRE, 4YRF, 4YRG, 4YRI, 4YRJ, 4YRK, 4YRL, 4YRM, 4YRN, 4YRO, 4YRP, 4YRQ, 4YRR, 4YRS, 4YRT

  • PubMed Abstract: 

    • American trypanosomiasis, commonly known as Chagas disease, is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. The chronic form of the infection often causes debilitating morbidity and mortality. However, the current treatment for the disease is typically inadequate owing to drug toxicity and poor efficacy, necessitating a continual effort to discover and develop new antiparasitic therapeutic agents ...

    American trypanosomiasis, commonly known as Chagas disease, is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. The chronic form of the infection often causes debilitating morbidity and mortality. However, the current treatment for the disease is typically inadequate owing to drug toxicity and poor efficacy, necessitating a continual effort to discover and develop new antiparasitic therapeutic agents. The structure of T. cruzi histidyl-tRNA synthetase (HisRS), a validated drug target, has previously been reported. Based on this structure and those of human cytosolic HisRS, opportunities for the development of specific inhibitors were identified. Here, efforts are reported to identify small molecules that bind to T. cruzi HisRS through fragment-based crystallographic screening in order to arrive at chemical starting points for the development of specific inhibitors. T. cruzi HisRS was soaked into 68 different cocktails from the Medical Structural Genomics of Pathogenic Protozoa (MSGPP) fragment library and diffraction data were collected to identify bound fragments after soaking. A total of 15 fragments were identified, all bound to the same site on the protein, revealing a fragment-binding hotspot adjacent to the ATP-binding pocket. On the basis of the initial hits, the design of reactive fragments targeting the hotspot which would be simultaneously covalently linked to a cysteine residue present only in trypanosomatid HisRS was initiated. Inhibition of T. cruzi HisRS was observed with the resultant reactive fragments and the anticipated binding mode was confirmed crystallographically. These results form a platform for the development of future generations of selective inhibitors for trypanosomatid HisRS.

    Organizational Affiliation: 

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidyl-tRNA synthetaseA, B456Trypanosoma cruzi strain CL BrenerMutation(s): 0 
Gene Names: Tc00.1047053507019.40
EC: 6.1.1.21
UniProt
Find proteins for Q4DA54 (Trypanosoma cruzi (strain CL Brener))
Explore Q4DA54 
Go to UniProtKB:  Q4DA54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4DA54
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HIS
Query on HIS
Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]		HISTIDINE
C6 H10 N3 O2
HNDVDQJCIGZPNO-YFKPBYRVSA-O		 Ligand Interaction
4JL
Query on 4JL
Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]		(4-chlorophenyl)methanol
C7 H7 Cl O
PTHGDVCPCZKZKR-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
N [auth B],
O [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
P [auth B],
Q [auth B]		DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.91α = 90
b = 118.736β = 91.45
c = 93.705γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Structure summary