5G3M | pdb_00005g3m

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

PDB DOI: https://doi.org/10.2210/pdb5G3M/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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: 1.85 Å
R-Value Free:
0.232 (Depositor), 0.235 (DCC)
R-Value Work:
0.199 (Depositor), 0.205 (DCC)
R-Value Observed:
0.200 (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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.6b00188
Primary Citation 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: 29.74 kDa
Atom Count: 2,177
Modeled Residue Count: 246
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GROUP 10 SECRETORY PHOSPHOLIPASE A2	A, B	123	Homo sapiens	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O15496
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
9JH Query on 9JH Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain N [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain N [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain N [auth A]	AA [auth B], N [auth A]	4-BENZYLBENZAMIDE C₁₄ H₁₃ N O BGTIIRYHWGADFD-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain N [auth A] Interactions & Density Focus chain AA [auth B] Focus chain N [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
9JH	BindingDB: 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 (Depositor), 0.235 (DCC)
R-Value Work: 0.199 (Depositor), 0.205 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.57	α = 90
b = 85.122	β = 90
c = 103.316	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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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