5G3M

Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of Azd2716: A Novel Secreted Phospholipase A2 (Spla2) Inhibitor for the Treatment of Coronary Artery Disease

Giordanetto, F.Pettersen, D.Starke, I.Nordberg, P.Dahlstrom, M.Knerr, L.Selmi, N.Rosengren, B.Larsson, L.O.Sandmark, J.Castaldo, M.Dekker, N.Karlsson, U.Hurt-Camejo, E.

(2016) ACS Med Chem Lett 7: 884

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00188
  • Primary Citation of Related Structures:  
    5G3M, 5G3N

  • PubMed Abstract: 

    Expedited structure-based optimization of the initial fragment hit 1 led to the design of ( R )- 7 (AZD2716) a novel, potent secreted phospholipase A 2 (sPLA 2 ) inhibitor with excellent preclinical pharmacokinetic properties across species, clear in vivo efficacy, and minimized safety risk. Based on accumulated profiling data, ( R )- 7 was selected as a clinical candidate for the treatment of coronary artery disease.


  • Organizational Affiliation

    Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit Departments of Medicinal Chemistry, Bioscience, DMPK, Discovery Sciences Departments of Structure & Biophysics, Reagents and Assay Development, and Screening Sciences and Sample Management, Astrazeneca, Mölndal , Pepparedsleden 1, SE-431 83 Mölndal, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GROUP 10 SECRETORY PHOSPHOLIPASE A2
A, B
123Homo sapiensMutation(s): 0 
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
9JH
Query on 9JH

Download Ideal Coordinates CCD File 
AA [auth B],
N [auth A]
4-BENZYLBENZAMIDE
C14 H13 N O
BGTIIRYHWGADFD-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.57α = 90
b = 85.122β = 90
c = 103.316γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary