E3Docker 2.0

HKMTi-1-005

E3L057878

Internal ID: BDB057878

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB057878/BDB057878.sdf

Basic Properties

Compound ID

E3L057878

Internal ID

BDB057878

Molecular formula

C27H36N6O2

Molecular weight

476.625000

Exact mass

476.289974

XLogP

3.4753

TPSA

65.9900

HBA / HBD

8 / 1

Rotatable bonds

Heavy atoms / rings

35 / 5

Activity summary

IC50 unknown 41000.00000000 nM
6 activity record(s) imported

InChIKey

LDFAJFPHFKEJOI-UHFFFAOYSA-N

SMILES

COc1cc2nc(N3CCN(C)CC3)nc(NC3CCN(Cc4ccccc4)CC3)c2cc1OC

Aliases

BDBM50498655 (preferred) HKMTi-1-005 (source_name) BDBM50498655 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
O96028	NSD2;KIAA1090;MMSET;TRX5;WHSC1 Histone-lysine N-methyltransferase NSD2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50498655	medium ; target=Histone-lysine N-methyltransferase NSD2
Q96L73	NSD1;ARA267;KMT3B Histone-lysine N-methyltransferase, H3 lysine-36 specific	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50498655	medium ; target=Histone-lysine N-methyltransferase, H3 lysine-36 specific
Q9BZ95	NSD3;WHSC1L1;DC28 Histone-lysine N-methyltransferase NSD3	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50498655	medium ; target=Histone-lysine N-methyltransferase NSD3

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50498655	Open	-	10.1016/j.ejmech.2021.113592; 10.1016/j.ejmech.2023.115440 PMID: 34147909; 37182335
PubChem	CID53315436	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	COc1cc2nc(N3CCN(C)CC3)nc(NC3CCN(Cc4ccccc4)CC3)c2cc1OC	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB057878/BDB057878.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB057878/BDB057878.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB057878/BDB057878.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB057878/BDB057878.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB057878/BDB057878.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50498655	IC50	41000 nM	Low	DOI: 10.1016/j.ejmech.2021.113592 PMID: 34147909	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50498655	IC50	41000 nM	Low	DOI: 10.1016/j.ejmech.2023.115440 PMID: 37182335	1
Histone-lysine N-methyltransferase NSD3 Q9BZ95 E3 ligase component	BindingDB:BDBM50498655	IC50	95000 nM	Low	DOI: 10.1016/j.ejmech.2023.115440 PMID: 37182335	1
Histone-lysine N-methyltransferase NSD3 Q9BZ95 E3 ligase component	BindingDB:BDBM50498655	IC50	95000 nM	Low	DOI: 10.1016/j.ejmech.2021.113592 PMID: 34147909	1
Histone-lysine N-methyltransferase, H3 lysine-36 specific Q96L73 E3 ligase component	BindingDB:BDBM50498655	IC50	112000 nM	Low	DOI: 10.1016/j.ejmech.2023.115440 PMID: 37182335	1
Histone-lysine N-methyltransferase, H3 lysine-36 specific Q96L73 E3 ligase component	BindingDB:BDBM50498655	IC50	112000 nM	Low	DOI: 10.1016/j.ejmech.2021.113592 PMID: 34147909	1