Resolved chemical identity

MRT866

Studied + deposited research ligand

Complete deposited identity retained; no connectivity-only or name-only merge.

1 assay / association records1 preparations2 research-ligand PDB entries

Clinical / development status: Not independently curated. A chemical probe classification does not imply medicinal approval.

Identity is separate from preparation

Chemical identity

Stable identity: INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N
Full InChIKey: XPHOPAPMJBSLFN-UHFFFAOYSA-N
Source identity status: complete deposited InChIKey
Deposited CCD identifiers: Y6V
External identifiers: See deposited identity and source links

Reference formula: C17H16N2O3S
Calculated molecular weight: 328.393
Calculated descriptors: cLogP 2.8838 · TPSA 58.64 Å² · HBD 1 · HBA 4RDKit 2025.09.3; calculations for this source identity, not experimental measurements.
Depiction validation: verified smiles full inchikey match

SMILES, InChI & complete identity record

Isomeric SMILES: c1cc(sc1)CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4
InChI: Not curated

{
  "aliases": [
    "~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide"
  ],
  "ccd_ids": [
    "Y6V"
  ],
  "ccd_names": "[\"~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide\"]",
  "ccd_types": "[\"non-polymer\"]",
  "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N",
  "connectivity_block": "XPHOPAPMJBSLFN",
  "curated_source_sha256": null,
  "curation_version": "frozen-v1.2",
  "external_identifiers": {},
  "formal_charge_by_ccd": "{\"Y6V\": 0}",
  "formulae": "[\"C17 H16 N2 O3 S\"]",
  "geometry_note": "CCD ideal SDF is a reference chemical geometry, not a deposited bound pose.",
  "identity_status": "complete_deposited_InChIKey",
  "inchikey": "XPHOPAPMJBSLFN-UHFFFAOYSA-N",
  "inventory_origin": "v1_CCD_inventory",
  "isomeric_smiles": "c1cc(sc1)CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4",
  "primary_name": "~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide",
  "retrieval_date": "2026-10-24",
  "smiles_stereo_by_ccd": "{\"Y6V\": \"c1cc(sc1)CN(C2CC2)C(=O)c3ccc4c(c3)OCC(=O)N4\"}",
  "source_metadata_sha256": "{\"Y6V\": \"2c8c70a80727afc9def58f2457cc063473f3c173b932c7f3f315681b62fe8a5e\"}",
  "source_urls": [
    "https://www.rcsb.org/ligand/Y6V"
  ]
}

Source aliases (2)

MRT866
~{N}-cyclopropyl-3-oxidanylidene-~{N}-(thiophen-2-ylmethyl)-4~{H}-1,4-benzoxazine-7-carboxamide

Measured target and original context

Bioactivity & experimental observations

Download assay CSV

Each row is one source-specific observation. Repeated measurements of this compound are not independent compounds. Direct binding, functional displacement and cellular outcomes retain their distinct endpoints.

Preparation	Tested target & construct	Method / endpoint	Original observation	Conditions & uncertainty	Source & verification
MRT866PREP:MRT866	NSD2 PWWP1 Construct not curatedHomo sapiens	KdSPR Kddirect binding affinity	= 349 ± 19 nM0.349 µM · exact unit conversion	Experimental context Replicates Not curated Uncertainty definition Not curated; do not assume SD or SEM Temperature — Buffer Not curated Conditions {} Qualification 349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.	PMID:34782742 · 2022Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained Original observation record { "DMSO_percent": null, "abstract_reported_endpoint": null, "abstract_reported_method": null, "abstract_reported_units": null, "abstract_reported_value": null, "assay_construct_end": null, "assay_construct_start": null, "assay_record_id": "PWWP:ASSAY:0003", "assay_type": "SPR Kd", "assay_value_transferred_to_modeled_stereoisomers": 0, "audit_decision": "retain_with_explicit_endpoint_and_identity", "baseline_assay_record": 1, "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0003\", \"assay_type\": \"SPR Kd\", \"ccd_id\": \"Y6V\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"MRT866\", \"conditions\": {}, \"domain\": \"PWWP1\", \"evidence_location\": \"Results: Discovery of a potent ligand targeting NSD2-PWWP1\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/\", \"gene\": \"NSD2\", \"interpretation\": \"\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"7MDN\", \"reference_id\": \"PMID:34782742\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 19, \"units\": \"nM\", \"value\": 349, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}", "buffer": null, "ccd_id": "Y6V", "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json", "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N", "chemical_identity_status": "exact_single_CCD_identity", "component_context": null, "compound_name": "MRT866", "conditions": "{}", "crystallographic_component_ids": null, "domain": "PWWP1", "domain_id": "UP:O96028:PWWP1", "endpoint_label_status": null, "evidence_class": "direct_binding_affinity", "evidence_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1", "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/", "gene": "NSD2", "interpretation": null, "molecular_entity_type": "small_molecule_preparation", "numeric_transcription_status": "matches_primary_report", "numeric_value_inferred_from_structure": 0, "pH": null, "pdb_id": "7MDN", "preparation_id": "PREP:MRT866", "protein_id": "UP:O96028", "qualitative_result": null, "reference_id": "PMID:34782742", "remaining_uncertainty": "349 \u00b1 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211\u2013350 is not assigned as the binding-assay construct.", "replicates": null, "role": "experimentally_studied_ligand", "source_component_url": null, "source_id": "S02", "source_reported_uncertainty": "19", "source_reported_units": "nM", "source_reported_value": "349", "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained", "temperature_C": null, "uncertainty": 19.0, "uncertainty_type": null, "uncertainty_uM": 0.019, "unit_conversion": null, "units": "nM", "value": 349.0, "value_operator": "=", "value_uM": 0.349, "verification_level": "primary_full_text_sections_verified" }

Preparation

Tested target & construct

Method / endpoint

Original observation

Conditions & uncertainty

Source & verification

MRT866PREP:MRT866

NSD2 PWWP1
Construct not curatedHomo sapiens

KdSPR Kddirect binding affinity

= 349 ± 19 nM0.349 µM · exact unit conversion

Experimental context

Replicates: Not curated
Uncertainty definition: Not curated; do not assume SD or SEM
Temperature: —
Buffer: Not curated
Conditions: {}
Qualification: 349 ± 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211–350 is not assigned as the binding-assay construct.

PMID:34782742 · 2022Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained

Original observation record

{
  "DMSO_percent": null,
  "abstract_reported_endpoint": null,
  "abstract_reported_method": null,
  "abstract_reported_units": null,
  "abstract_reported_value": null,
  "assay_construct_end": null,
  "assay_construct_start": null,
  "assay_record_id": "PWWP:ASSAY:0003",
  "assay_type": "SPR Kd",
  "assay_value_transferred_to_modeled_stereoisomers": 0,
  "audit_decision": "retain_with_explicit_endpoint_and_identity",
  "baseline_assay_record": 1,
  "baseline_original": "{\"assay_record_id\": \"PWWP:ASSAY:0003\", \"assay_type\": \"SPR Kd\", \"ccd_id\": \"Y6V\", \"ccd_mapping_source\": \"Provenance/Literature/ligand_ccd_associations.json\", \"compound_name\": \"MRT866\", \"conditions\": {}, \"domain\": \"PWWP1\", \"evidence_location\": \"Results: Discovery of a potent ligand targeting NSD2-PWWP1\", \"evidence_url\": \"https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/\", \"gene\": \"NSD2\", \"interpretation\": \"\", \"numeric_value_inferred_from_structure\": false, \"pdb_id\": \"7MDN\", \"reference_id\": \"PMID:34782742\", \"role\": \"experimentally_studied_ligand\", \"uncertainty\": 19, \"units\": \"nM\", \"value\": 349, \"value_operator\": \"=\", \"verification_level\": \"primary_full_text_sections_verified\"}",
  "buffer": null,
  "ccd_id": "Y6V",
  "ccd_mapping_source": "Provenance/Literature/ligand_ccd_associations.json",
  "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N",
  "chemical_identity_status": "exact_single_CCD_identity",
  "component_context": null,
  "compound_name": "MRT866",
  "conditions": "{}",
  "crystallographic_component_ids": null,
  "domain": "PWWP1",
  "domain_id": "UP:O96028:PWWP1",
  "endpoint_label_status": null,
  "evidence_class": "direct_binding_affinity",
  "evidence_location": "Results: Discovery of a potent ligand targeting NSD2-PWWP1",
  "evidence_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/",
  "gene": "NSD2",
  "interpretation": null,
  "molecular_entity_type": "small_molecule_preparation",
  "numeric_transcription_status": "matches_primary_report",
  "numeric_value_inferred_from_structure": 0,
  "pH": null,
  "pdb_id": "7MDN",
  "preparation_id": "PREP:MRT866",
  "protein_id": "UP:O96028",
  "qualitative_result": null,
  "reference_id": "PMID:34782742",
  "remaining_uncertainty": "349 \u00b1 19 nM verified in Results; MRT866-specific SPR construct/protocol, replicate definition and uncertainty statistic remain unresolved. Crystallography 211\u2013350 is not assigned as the binding-assay construct.",
  "replicates": null,
  "role": "experimentally_studied_ligand",
  "source_component_url": null,
  "source_id": "S02",
  "source_reported_uncertainty": "19",
  "source_reported_units": "nM",
  "source_reported_value": "349",
  "source_verification_scope": "Phase 3 primary full-text Methods, Results and figure legends through official NCBI BioC; actual publisher supplement; assay-specific scope retained",
  "temperature_C": null,
  "uncertainty": 19.0,
  "uncertainty_type": null,
  "uncertainty_uM": 0.019,
  "unit_conversion": null,
  "units": "nM",
  "value": 349.0,
  "value_operator": "=",
  "value_uM": 0.349,
  "verification_level": "primary_full_text_sections_verified"
}

Exact deposited instances

Experimental structures

Native-core and broader Pfam proximity are distinguished from contacts elsewhere in a protein. Each action opens the actual deposited ligand instance. Geometric proximity does not supply a measured binding affinity.

Entry / ligand	Native domain & protein chain	Geometric evidence	Minimum distance	Inspect
7LMT · Y6VPDB:7LMT:LIG:I:Y6V:401:.	NSD2 PWWP1Protein label chain A · ligand label chain I	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9985 Å Pfam: 2.9947 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:I:Y6V:401:.	NSD2 PWWP1Protein label chain H · ligand label chain I	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.8559 Å Pfam: 3.504 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:K:Y6V:401:.	NSD2 PWWP1Protein label chain B · ligand label chain K	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.0038 Å Pfam: 2.9635 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:K:Y6V:401:.	NSD2 PWWP1Protein label chain C · ligand label chain K	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.939 Å Pfam: 3.4868 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:L:Y6V:401:.	NSD2 PWWP1Protein label chain C · ligand label chain L	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.0005 Å Pfam: 3.0005 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:L:Y6V:401:.	NSD2 PWWP1Protein label chain D · ligand label chain L	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.7989 Å Pfam: 3.5337 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:M:Y6V:401:.	NSD2 PWWP1Protein label chain D · ligand label chain M	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.8696 Å Pfam: 2.8696 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:M:Y6V:401:.	NSD2 PWWP1Protein label chain E · ligand label chain M	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.9198 Å Pfam: 3.5829 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:N:Y6V:401:.	NSD2 PWWP1Protein label chain B · ligand label chain N	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.8907 Å Pfam: 3.4734 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:N:Y6V:401:.	NSD2 PWWP1Protein label chain E · ligand label chain N	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9718 Å Pfam: 2.9677 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:P:Y6V:401:.	NSD2 PWWP1Protein label chain A · ligand label chain P	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.9491 Å Pfam: 3.4802 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:P:Y6V:401:.	NSD2 PWWP1Protein label chain F · ligand label chain P	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9918 Å Pfam: 2.9914 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:Q:Y6V:401:.	NSD2 PWWP1Protein label chain F · ligand label chain Q	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.9203 Å Pfam: 3.4866 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:Q:Y6V:401:.	NSD2 PWWP1Protein label chain G · ligand label chain Q	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9609 Å Pfam: 2.9609 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:R:Y6V:401:.	NSD2 PWWP1Protein label chain G · ligand label chain R	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.9131 Å Pfam: 3.536 Å	View deposited instance
7LMT · Y6VPDB:7LMT:LIG:R:Y6V:401:.	NSD2 PWWP1Protein label chain H · ligand label chain R	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9704 Å Pfam: 2.9704 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:I:Y6V:401:.	NSD2 PWWP1Protein label chain A · ligand label chain I	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9387 Å Pfam: 2.9387 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:I:Y6V:401:.	NSD2 PWWP1Protein label chain H · ligand label chain I	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.8394 Å Pfam: 3.5194 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:K:Y6V:401:.	NSD2 PWWP1Protein label chain B · ligand label chain K	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9349 Å Pfam: 2.9349 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:K:Y6V:401:.	NSD2 PWWP1Protein label chain C · ligand label chain K	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.9046 Å Pfam: 3.4641 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:L:Y6V:401:.	NSD2 PWWP1Protein label chain C · ligand label chain L	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9281 Å Pfam: 2.9281 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:L:Y6V:401:.	NSD2 PWWP1Protein label chain D · ligand label chain L	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.7861 Å Pfam: 3.5234 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:M:Y6V:401:.	NSD2 PWWP1Protein label chain D · ligand label chain M	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.8206 Å Pfam: 2.8206 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:M:Y6V:401:.	NSD2 PWWP1Protein label chain E · ligand label chain M	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.8855 Å Pfam: 3.5464 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:N:Y6V:401:.	NSD2 PWWP1Protein label chain B · ligand label chain N	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.8567 Å Pfam: 3.4955 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:N:Y6V:401:.	NSD2 PWWP1Protein label chain E · ligand label chain N	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9125 Å Pfam: 2.9125 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:P:Y6V:401:.	NSD2 PWWP1Protein label chain A · ligand label chain P	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.951 Å Pfam: 3.4898 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:P:Y6V:401:.	NSD2 PWWP1Protein label chain F · ligand label chain P	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9307 Å Pfam: 2.9307 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:Q:Y6V:401:.	NSD2 PWWP1Protein label chain F · ligand label chain Q	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.8794 Å Pfam: 3.4941 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:Q:Y6V:401:.	NSD2 PWWP1Protein label chain G · ligand label chain Q	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.9056 Å Pfam: 2.9056 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:R:Y6V:401:.	NSD2 PWWP1Protein label chain G · ligand label chain R	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 3.9208 Å Pfam: 3.5515 Å	View deposited instance
7MDN · Y6VPDB:7MDN:LIG:R:Y6V:401:.	NSD2 PWWP1Protein label chain H · ligand label chain R	native annotation core contactexperimentally studied ligandreported studied structural ligand · research ligand. Deposited geometry is not solution affinity.	Core: 2.8979 Å Pfam: 2.8979 Å	View deposited instance

Preparations, identities and controls remain separate

Experimental context

MRT866

PREP:MRT866

Complete deposited identity retained; no connectivity-only or name-only merge.

assay preparation

Complete preparation record

{
  "chemical_id": "INCHIKEY:XPHOPAPMJBSLFN-UHFFFAOYSA-N",
  "entity_type": "small_molecule_preparation",
  "exact_ccd_id": "Y6V",
  "identity_note": "Complete deposited identity retained; no connectivity-only or name-only merge.",
  "identity_status": "exact_single_CCD_identity",
  "modeled_candidate_ccd_ids": "[]",
  "modeled_candidate_chemical_ids": "[]",
  "name": "MRT866",
  "preparation_id": "PREP:MRT866",
  "role": "assay_preparation",
  "sequence_if_defined": null
}

Provenance and reproducibility

Sources & downloads

https://pmc.ncbi.nlm.nih.gov/articles/PMC9189931/https://www.rcsb.org/ligand/Y6V

Download complete evidence JSON Curation methods & source receipts

Snapshot 2026-10-26 · phase5-1.0.0 · original measurements, operators, constructs and uncertainty are retained in the exports.