6G5J

Secreted phospholipase A2 type X in complex with ligand

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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Ligand Structure Quality Assessment 


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Literature

Design of Selective sPLA2-X Inhibitor (-)-2-{2-[Carbamoyl-6-(trifluoromethoxy)-1H-indol-1-yl]pyridine-2-yl}propanoic Acid.

Giordanetto, F., Knerr, L., Nordberg, P., Pettersen, D., Selmi, N., Beisel, H.G., de la Motte, H., Mansson, A., Dahlstrom, M., Broddefalk, J., Saarinen, G., Klingegard, F., Hurt-Camejo, E., Rosengren, B., Wikstrom, J., Wagberg, M., Brengdahl, J., Rohman, M., Sandmark, J., Akerud, T., Roth, R.G., Jansen, F., Ahlqvist, M.

(2018) ACS Med Chem Lett 9: 600-605

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00507
  • Primary Citation of Related Structures:  
    6G5J

  • PubMed Abstract: 

    • A lead generation campaign identified indole-based sPLA 2 -X inhibitors with a promising selectivity profile against other sPLA 2 isoforms. Further optimization of sPLA 2 selectivity and metabolic stability resulted in the design of (-)- 17 , a novel, potent, and selective sPLA 2 -X inhibitor with an exquisite pharmacokinetic profile characterized by high absorption and low clearance, and low toxicological risk ...

    A lead generation campaign identified indole-based sPLA 2 -X inhibitors with a promising selectivity profile against other sPLA 2 isoforms. Further optimization of sPLA 2 selectivity and metabolic stability resulted in the design of (-)- 17 , a novel, potent, and selective sPLA 2 -X inhibitor with an exquisite pharmacokinetic profile characterized by high absorption and low clearance, and low toxicological risk. Compound (-)- 17 was tested in an ApoE -/- murine model of atherosclerosis to evaluate the effect of reversible, pharmacological sPLA 2 -X inhibition on atherosclerosis development. Despite being well tolerated and achieving adequate systemic exposure of mechanistic relevance, (-)- 17 did not significantly affect circulating lipid and lipoprotein biomarkers and had no effect on coronary function or histological markers of atherosclerosis.

    Organizational Affiliation: 

    Medicinal Chemistry, Translational Sciences, Bioscience, and Drug Metabolism and Pharmacokinetics, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca, Gothenburg SE-431 89, Sweden.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Group 10 secretory phospholipase A2A, B165Homo sapiensMutation(s): 0 
Gene Names: PLA2G10
EC: 3.1.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for O15496 (Homo sapiens)
Explore O15496 
Go to UniProtKB:  O15496
PHAROS:  O15496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15496
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EM8 (Subject of Investigation/LOI)
Query on EM8
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth B]		(3~{R})-3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]butanoic acid
C20 H17 F3 N2 O4
OSJXLDOVNXZNHD-LLVKDONJSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
F [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EM8 Binding MOAD:  6G5J IC50: 200 (nM) from 1 assay(s)
BindingDB:  6G5J IC50: 200 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.962α = 90
b = 85.501β = 90
c = 103.079γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release