8S00 | pdb_00008s00

CpKRS complexed with lysine and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.222 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8S00

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Literature

Cryptosporidium lysyl-tRNA synthetase inhibitors define the interplay between solubility and permeability required to achieve efficacy.

Caldwell, N.Peet, C.Miller, P.Colon, B.L.Taylor, M.G.Cocco, M.Dawson, A.Lukac, I.Teixeira, J.E.Robinson, L.Frame, L.Seizova, S.Damerow, S.Tamaki, F.Post, J.Riley, J.Mutter, N.Hanna, J.C.Ferguson, L.Hu, X.Tinti, M.Forte, B.Norcross, N.R.Campbell, P.S.Svensen, N.Caldwell, F.C.Jansen, C.Postis, V.Read, K.D.Huston, C.D.Gilbert, I.H.Baragana, B.Pawlowic, M.C.

(2024) Sci Transl Med 16: eadm8631-eadm8631

  • DOI: https://doi.org/10.1126/scitranslmed.adm8631
  • Primary Citation Related Structures: 
    8R2A, 8S00

  • PubMed Abstract: 

    Cryptosporidiosis is a diarrheal disease caused by infection with Cryptosporidium spp. parasites and is a leading cause of death in malnourished children worldwide. The only approved treatment, nitazoxanide, has limited efficacy in this at-risk patient population. Additional safe therapeutics are urgently required to tackle this unmet medical need. However, the development of anti-cryptosporidial drugs is hindered by a lack of understanding of the optimal compound properties required to treat this gastrointestinal infection. To address this knowledge gap, a diverse set of potent lysyl-tRNA synthetase inhibitors was profiled to identify optimal physicochemical and pharmacokinetic properties required for efficacy in a chronic mouse model of infection. The results from this comprehensive study illustrated the importance of balancing solubility and permeability to achieve efficacy in vivo. Our results establish in vitro criteria for solubility and permeability that are predictive of compound efficacy in vivo to guide the optimization of anti-cryptosporidial drugs. Two compounds from chemically distinct series (DDD489 and DDD508) were identified as demonstrating superior efficacy and prioritized for further evaluation. Both compounds achieved marked parasite reduction in immunocompromised mouse models and a disease-relevant calf model of infection. On the basis of these promising data, these compounds have been selected for progression to preclinical safety studies, expanding the portfolio of potential treatments for this neglected infectious disease.


  • Organizational Affiliation
    • Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

Macromolecule Content 

  • Total Structure Weight: 124.55 kDa 
  • Atom Count: 8,921 
  • Modeled Residue Count: 1,003 
  • Deposited Residue Count: 1,070 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase
A, B
535Cryptosporidium parvum IowaMutation(s): 0 
Gene Names: cgd4_2370
EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CR27 
Go to UniProtKB:  Q5CR27
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5CR27
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H4W
(Subject of Investigation/LOI)

Query on A1H4W



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]
6-oxidanyl-~{N}-[(1-oxidanylcyclohexyl)methyl]-4-oxidanylidene-chromene-2-carboxamide
C17 H19 N O5
LEGRYHJSBGMPHH-UHFFFAOYSA-N
LYS

Query on LYS



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
TRS

Query on TRS



Download:Ideal Coordinates CCD File
E [auth A],
L [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A],
I [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.222 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.182 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.987α = 90
b = 121.761β = 90
c = 143.092γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
UK Research and Innovation (UKRI)United KingdomMR/S01970/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 2.0: 2025-07-09
    Type: Coordinate replacement
    Reason: Ligand geometry
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary