5OW8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Group 10 secretory phospholipase A2A, B123Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AYN (Subject of Investigation/LOI)
Query on AYN

Download Ideal Coordinates CCD File 
H [auth A],
T [auth B]
1-[3-(trifluoromethyl)phenyl]indole-2-carboxamide
C16 H11 F3 N2 O
IRJUBZXSBPCNAU-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A],
K [auth A],
L [auth A],
U [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A],
P [auth B],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
O [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
M [auth A],
N [auth A],
V [auth B],
W [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
AYN Binding MOAD:  5OW8 IC50: 6900 (nM) from 1 assay(s)
BindingDB:  5OW8 IC50: 6900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.652α = 90
b = 85.367β = 90
c = 102.954γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



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