5OWC

Indole-2 carboxamides as selective secreted phospholipase A2 type X (sPLA2-X) inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of a Series of Indole-2 Carboxamides as Selective Secreted Phospholipase A2Type X (sPLA2-X) Inhibitors.

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

(2018) ACS Med Chem Lett 9: 594-599

  • DOI: https://doi.org/10.1021/acsmedchemlett.7b00505
  • Primary Citation of Related Structures:  
    5OW8, 5OWC

  • PubMed Abstract: 

    In order to assess the potential of sPLA 2 -X as a therapeutic target for atherosclerosis, novel sPLA 2 inhibitors with improved type X selectivity are required. To achieve the objective of identifying such compounds, we embarked on a lead generation effort that resulted in the identification of a novel series of indole-2-carboxamides as selective sPLA2-X inhibitors with excellent potential for further optimization.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Group 10 secretory phospholipase A2
A, B
122Homo 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
GTEx:  ENSG00000069764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15496
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AYZ (Subject of Investigation/LOI)
Query on AYZ

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
3-[3-[2-aminocarbonyl-6-(trifluoromethyloxy)indol-1-yl]phenyl]propanoic acid
C19 H15 F3 N2 O4
YOCROJNDVYFOIL-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
O [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
P [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
M [auth B],
N [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.85α = 90
b = 86.51β = 90
c = 103.44γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Structure summary