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 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


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: 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
Find similar proteins by:  (by identity cutoff)  |  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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EM8
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EM8IC50:  200   nM  Binding MOAD
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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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