E3Docker 2.0

4-cyano-N-cyclopropyl-N-(thiophen-2-ylmethyl)benzamide

E3L060657

Internal ID: BDB060657

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB060657/BDB060657.sdf

Basic Properties

Compound ID

E3L060657

Internal ID

BDB060657

Molecular formula

C16H14N2OS

Molecular weight

282.368000

Exact mass

282.082684

XLogP

3.4246

TPSA

44.1000

HBA / HBD

3 / 0

Rotatable bonds

Heavy atoms / rings

20 / 3

Activity summary

Kd unknown 91.00000000 nM
6 activity record(s) imported

InChIKey

WYAGGMZTARRIDX-UHFFFAOYSA-N

SMILES

N#Cc1ccc(C(=O)N(Cc2cccs2)C2CC2)cc1

Aliases

BDBM50562969 (preferred) 4-cyano-N-cyclopropyl-N-(thiophen-2-ylmethyl)benzamide (source_name) BDBM50562969 (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:BDBM50562969	medium ; target=Histone-lysine N-methyltransferase NSD2
Q9BZ95	NSD3;WHSC1L1;DC28 Histone-lysine N-methyltransferase NSD3	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50562969	medium ; target=Histone-lysine N-methyltransferase NSD3

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50562969	Open	-	10.1021/acs.jmedchem.0c01768; 10.7270/Q2PG1WRN; 10.1021/acs.jmedchem.3c00948 PMID: 33522809; 35704853; 37578463
PubChem	CID37484611	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	N#Cc1ccc(C(=O)N(Cc2cccs2)C2CC2)cc1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB060657/BDB060657.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB060657/BDB060657.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB060657/BDB060657.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB060657/BDB060657.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB060657/BDB060657.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50562969	IC50	17300 nM	Low	DOI: 10.1021/acs.jmedchem.0c01768 PMID: 33522809	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50562969	IC50	24670 nM	Low	DOI: 10.7270/Q2PG1WRN PMID: 35704853	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50562969	Kd	349 nM	Moderate	DOI: 10.1021/acs.jmedchem.3c00948 PMID: 37578463	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50562969	Kd	7000 nM	Low	DOI: 10.1021/acs.jmedchem.0c01768 PMID: 33522809	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50562969	Kd	3400 nM	Low	DOI: 10.1021/acs.jmedchem.0c01768 PMID: 33522809	1
Histone-lysine N-methyltransferase NSD3 Q9BZ95 E3 ligase component	BindingDB:BDBM50562969	Kd	91 nM	High	DOI: 10.7270/Q2PG1WRN PMID: 35704853	1