8R2A

CpKRS complexed with lysine and an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysine--tRNA ligaseA,
B [auth D],
C,
D [auth B]
534Cryptosporidium parvumMutation(s): 0 
Gene Names: CPATCC_001825
EC: 6.1.1.6
UniProt
Find proteins for A0A7S7RG57 (Cryptosporidium parvum)
Explore A0A7S7RG57 
Go to UniProtKB:  A0A7S7RG57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7S7RG57
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XLQ (Subject of Investigation/LOI)
Query on XLQ

Download Ideal Coordinates CCD File 
E [auth A],
I [auth D],
M [auth C],
S [auth B]
2-azanyl-4-(trifluoromethyl)-6-[[(1~{R},3~{S})-3-(trifluoromethyl)cyclohexyl]methyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
C15 H16 F6 N4 O
MHHCFMCEGSPNMQ-UHFFFAOYSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
H [auth A],
L [auth D],
R [auth C],
U [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
P [auth C],
Q [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth D],
N [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A],
K [auth D],
O [auth C],
T [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.099α = 90
b = 118.667β = 90.376
c = 142.837γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/S019170/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release