5OW8

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

PDB DOI: https://doi.org/10.2210/pdb5OW8/pdb

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

Deposited: 2017-08-31 Released: 2018-08-01
Deposition Author(s): Sandmark, J.S., Roth, R.G., Knerr, L., Bodin, C., Pettersen, D.

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 1.2 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

PubMed: 30034585 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/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.

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.

Macromolecule Content

Total Structure Weight: 29.28 kDa
Atom Count: 2,132
Modelled Residue Count: 246
Deposited Residue Count: 246
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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 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 GTEx: ENSG00000069764
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15496
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AYN (Subject of Investigation/LOI) Query on AYN Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain T [auth B] MOL2 format, chain H [auth A] MOL2 format, chain T [auth B] mmCIF format, chain H [auth A] mmCIF format, chain T [auth B]	H [auth A], T [auth B]	1-[3-(trifluoromethyl)phenyl]indole-2-carboxamide C₁₆ H₁₁ F₃ N₂ O IRJUBZXSBPCNAU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain T [auth B] Interactions & Density Focus chain H [auth A] Focus chain T [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File 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 U [auth B] 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 U [auth B] 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 U [auth B]	I [auth A], J [auth A], K [auth A], L [auth A], U [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain U [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain U [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 G [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	M [auth A], N [auth A], V [auth B], W [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain V [auth B] Focus chain W [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
AYN	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 = 27.652	α = 90
b = 85.367	β = 90
c = 102.954	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-08-01

Deposition Author(s):

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
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Structure summary