ebselen

CHEBI:77543 ·resolve ·ANTIBACTERIAL ·EXACT SEEDED

A benzoselenazole that is 1,2-benzoselenazol-3-one carrying an additional phenyl substituent at position 2. Acts as a mimic of glutathione peroxidase. — ChEBI

Machine-generated and unreviewed. Identity, structure and cross-references come straight from ChEBI's and CARD's own data; no curator has signed off on this record yet.

Classification

Strictly broader compounds or drug classes this molecule belongs to.

CHEBI:78151 CHEBI:78151

Chemical structure

Computed structure properties
Molecular formula	C13H9NOSe
Charge	0
Average mass	274.181 Da
Monoisotopic mass	274.98494 Da
Source	ChEBI
InChIKey	DYEFUKCXAQOFHX-UHFFFAOYSA-N

SMILES

O=c1c2ccccc2[se]n1-c1ccccc1

InChI

InChI=1S/C13H9NOSe/c15-13-11-8-4-5-9-12(11)16-14(13)10-6-2-1-3-7-10/h1-9H

Also called

ebseleno (INN)— chebi
ebselenum (INN)— chebi
ebsélène (INN)— chebi
2-phenyl-1,2-benzoselenazol-3(2H)-one (EXACT_SYNONYM)— chebi
2-phenyl-1,2-benzoselenazol-3-one (EXACT_SYNONYM)— chebi
DR-3305 (EXACT_SYNONYM)— chebi
DR3305 (EXACT_SYNONYM)— chebi
PZ 51 (EXACT_SYNONYM)— chebi
SPI-1005 (EXACT_SYNONYM)— chebi

Cross-references

Equivalent identifiers for this same structure in other resources.

cas:60940-34-3
chemspider:3082
drugbank:DB12610
lincs.smallmolecule:LSM-2644
reaxys:164926
wikipedia.en:Ebselen

Activity roles

Every antimicrobial role a source asserts for this compound — the unreduced evidence behind its antimicrobial_class.

CHEBI:149553 CHEBI:149553
CHEBI:33282 CHEBI:33282
CHEBI:35718 CHEBI:35718

Source concepts

Every upstream concept that resolved to this record. The merge is the product: this is what shows ChEBI and CARD are describing the same structure.

Upstream concepts merged into this record
Source	Native ID	Label	Minted CURIE	Version
CHEBI	`CHEBI:77543`	ebselen	`antibioticmech:chebi-aa484a34c5`	2026-08-30

Molecular targets

The molecular entity or process this compound acts on. Each target carries evidence — this is a mechanistic claim, not a classification.

Genome polyprotein VIRAL_PROTEIN MEASURED_TARGET_ASSOCIATION

BindingDB quantitative measurement in the named target organism; source assay descriptions and identifiers are retained per measurement. Evidence status: PRIMARY_EVIDENCE. Source: BINDINGDB 2026-09 (retrieved 2026-08-31).

Orthohepacivirus hominis NCBITaxon:3052230

Quantitative measurements
Type	Reported value	Assay	BindingDB IDs	Reference
IC50	1.4e+3 nM	EMSA Binding assays containing 25 mM MOPS pH 7.5, 1.25 mM MgCl2, 20 nM Cy5-dT15, and 200 nM NS3h_1b were incubated 5 min at RT. Following addition of indicated concentrations of ebselen, the binding reactions were incubated another 5 min at 23 C.	`RSID 251939` `assay 6323_1` `monomer 34233`	`PMID:25126694`

Organism-specific examples
Protein	Gene	Organism	Entry
Genome polyprotein `UniProtKB:A3EZJ3`	—	Orthohepacivirus hominis	UNREVIEWED

PMID:25126694 (BindingDB literature-curated quantitative target measurement; source value, assay text, reaction-set ID, and target organism retained.)

Replicase polyprotein 1ab VIRAL_PROTEIN MEASURED_TARGET_ASSOCIATION

Severe acute respiratory syndrome coronavirus 2 NCBITaxon:2697049

Quantitative measurements
Type	Reported value	Assay	BindingDB IDs	Reference
IC50	670 nM	high-throughput activity assay Recombinant SARS-CoV-2 Mpro with native N and C termini was expressed in Escherichia coli, and subsequently purified (Extended Data Fig. 1a, b). The molecular mass of SARS-CoV-2 Mpro as determined by mass spectroscopy is 33797.0 Da, consistent with its theoretical molecular mass of 33796.8 Da. To characterize the enzymatic activity of SARS-CoV-2 Mpro and to carry out high-throughput screening of inhibitors, we developed a fluorescence resonance energy transfer assay. To do this, we designed and synthesized the fluorescently labelled substrate Mca AVLQ↓SGFRK(Dnp)K, derived from the N-terminal autocleavage sequence of the viral protease, for time-dependent kinetic analysis (Extended Data Fig. 1e). The catalytic efficiency (kcat/Km) for SARS-CoV-2 Mpro was measured to be 28,500 M−1 s−1, which is slightly higher than that for SARS-CoV Mpro (kcat/Km = 26,500 M−1 s−1)10 and more than 30-fold higher than that of human rhinovirus 3C protease (kcat/Km = 920 M−1 s−1).	`RSID 840120` `assay 8774_1` `monomer 34233`	`PMID:32272481`
IC50	670 nM	No assay is provided This is a review article.	`RSID 868915` `assay 8918_1` `monomer 34233`	`PMID:32852058`
EC50	4670 nM	No assay is provided This is a review article.	`RSID 868916` `assay 8918_1` `monomer 34233`	`PMID:32852058`
IC50	80 nM	Hit profiling assay without DTT Primary assay principle based on quenched FRET peptide substrate of SARS-CoV-2 3CL-Pro (lhs). Inhibiting compounds reduce fluorescence signal relative to DMSO controls. Hit profiling using X-ray. Substrate turnover was directly proportional to enzyme concentrations up to 60 nM and assay incubation times up to 15 minutes post substrate addition.	`RSID 902201` `assay 9114_1` `monomer 34233`	`DOI:10.1101/2020.12.16.422677`
IC50	30 nM	Hit profiling assay without DTT Primary assay principle based on quenched FRET peptide substrate of SARS-CoV-2 3CL-Pro (lhs). Inhibiting compounds reduce fluorescence signal relative to DMSO controls. Hit profiling using X-ray. Substrate turnover was directly proportional to enzyme concentrations up to 60 nM and assay incubation times up to 15 minutes post substrate addition.	`RSID 902202` `assay 9114_1` `monomer 34233`	`DOI:10.1101/2020.12.16.422677`
IC50	520 nM	Various Assay This is a review article. Please point to the original journal.	`RSID 1073669` `assay 10079_1` `monomer 34233`	`PMID:34798775`
EC50	4670 nM	Various Assay This is a review article. Please point to the original journal.	`RSID 1073726` `assay 10079_1` `monomer 34233`	`PMID:34798775`
IC50	670 nM	Various Assay This is a review article. Please point to the original journal.	`RSID 1073727` `assay 10079_1` `monomer 34233`	`PMID:34798775`

Organism-specific examples
Protein	Gene	Organism	Entry
Replicase polyprotein 1ab `UniProtKB:P0DTD1`	—	Severe acute respiratory syndrome coronavirus 2	REVIEWED

PMID:32272481 (BindingDB literature-curated quantitative target measurement; source value, assay text, reaction-set ID, and target organism retained.)
PMID:32852058 (BindingDB literature-curated quantitative target measurement; source value, assay text, reaction-set ID, and target organism retained.)
DOI:10.1101/2020.12.16.422677 (BindingDB literature-curated quantitative target measurement; source value, assay text, reaction-set ID, and target organism retained.)
PMID:34798775 (BindingDB literature-curated quantitative target measurement; source value, assay text, reaction-set ID, and target organism retained.)

Mechanism summary

Mode of action: VIRAL_PROTEASE_INHIBITION microbial target — Assigned from ChEBI role CHEBI:147285 (EC 3.4.22.69 (SARS coronavirus main proteinase) inhibitor). ChEBI asserts the role on the compound, but this mechanism belongs to an anti-viral activity while the record is filed as ANTIBACTERIAL. Either the compound has both activities, or the filing is wrong — the priority table has put azole antifungals under ANTIBACTERIAL before now. A curator should decide which. The role names a target specific to the microbe or virus — see mode_of_action_target_scope. Not a curator's mechanistic review.

Curation history

SEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Seeded from data/raw/ inventories (CHEBI)
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-30 · seed_from_sources
Re-seeded from updated data/raw/ inventories
RESEEDED_FROM_SOURCES 2026-08-31 · seed_from_sources
Re-seeded from updated data/raw/ inventories

Provenance

Seeded by scripts/seed_from_sources.py from the committed inventories in data/raw/. View the record.