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 

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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 ...

    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
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(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
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / 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		 Ligand Interaction
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		 Ligand Interaction
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		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A],
Q [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9JH Binding MOAD:  5G3M IC50: 2200 (nM) from 1 assay(s)
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 


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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