5G3N | pdb_00005g3n

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

PDB DOI: https://doi.org/10.2210/pdb5G3N/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-04-29 Released: 2016-09-14
Deposition Author(s): Sandmark, J., Bodin, C., Hallberg, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.231 (Depositor), 0.232 (DCC)
R-Value Work:
0.195 (Depositor), 0.193 (DCC)
R-Value Observed:
0.197 (Depositor)

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

PubMed: 27774123 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 29.41 kDa
Atom Count: 2,238
Modelled Residue Count: 252
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHOLIPASE A2, MEMBRANE ASSOCIATED	A, B	127	Homo sapiens	Mutation(s): 2 EC: 3.1.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for P14555 (Homo sapiens) Explore P14555 Go to UniProtKB: P14555
PHAROS: P14555 GTEx: ENSG00000188257
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14555
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X28 Query on X28 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID C₂₃ H₂₁ N O₃ UHEGDWIZAOPGIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
X28	BindingDB: 5G3N	IC50: 12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.231 (Depositor), 0.232 (DCC)
R-Value Work: 0.195 (Depositor), 0.193 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.1	α = 90
b = 66.53	β = 90
c = 73.77	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-14

Deposition Author(s):

Sandmark, J.

Bodin, C.

Hallberg, K.

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