E3Docker 2.0

d]pyrimidin-4(3H)-one

E3L061016

Internal ID: BDB061016

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB061016/BDB061016.sdf

Basic Properties

Compound ID

E3L061016

Internal ID

BDB061016

Molecular formula

C25H26N4O4S

Molecular weight

478.574000

Exact mass

478.167476

XLogP

2.2893

TPSA

95.6000

HBA / HBD

7 / 1

Rotatable bonds

Heavy atoms / rings

34 / 6

Activity summary

IC50 unknown 132.00000000 nM
7 activity record(s) imported

InChIKey

ZJOXWRFJOUWUKX-GOSISDBHSA-N

SMILES

O=C1O[C@@H](C(=O)N2CCN(Cc3nc4sc5c(c4c(=O)[nH]3)CCCC5)CC2)Cc2ccccc21

Aliases

BDBM50572787 (preferred) d]pyrimidin-4(3H)-one (source_name) BDBM50572787 (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:BDBM50572787	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:BDBM50572787	medium ; target=Histone-lysine N-methyltransferase, H3 lysine-36 specific

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50572787	Open	-	10.1016/j.ejmech.2021.113592; 10.1021/acs.jmedchem.2c01920; 10.1021/acs.jmedchem.3c00948; 10.1016/j.ejmech.2023.115440; 10.1016/j.ejmech.2023.115232; 10.7270/Q2H70MGD PMID: 34147909; 36642961; 37578463; 37182335; 36863225; 38805937
PubChem	CID30843512	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C1O[C@@H](C(=O)N2CCN(Cc3nc4sc5c(c4c(=O)[nH]3)CCCC5)CC2)Cc2ccccc21	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB061016/BDB061016.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB061016/BDB061016.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB061016/BDB061016.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB061016/BDB061016.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB061016/BDB061016.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50572787	IC50	11200 nM	Low	DOI: 10.1016/j.ejmech.2021.113592 PMID: 34147909	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50572787	IC50	132 nM	Moderate	DOI: 10.7270/Q2H70MGD PMID: 38805937	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50572787	IC50	132000 nM	Low	DOI: 10.1021/acs.jmedchem.3c00948 PMID: 37578463	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50572787	IC50	132000 nM	Low	DOI: 10.1016/j.ejmech.2023.115440 PMID: 37182335	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50572787	IC50	132000 nM	Low	DOI: 10.1021/acs.jmedchem.2c01920 PMID: 36642961	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50572787	IC50	132000 nM	Low	DOI: 10.1016/j.ejmech.2023.115232 PMID: 36863225	1
Histone-lysine N-methyltransferase, H3 lysine-36 specific Q96L73 E3 ligase component	BindingDB:BDBM50572787	IC50	>1000000 nM	Low	DOI: 10.1021/acs.jmedchem.3c00948 PMID: 37578463	1