E3Docker 2.0

< Back to small molecule database

BDBM50440581

E3L056273

Internal ID: BDB056273

Activity data available Local docking-ready structure

Dock with P29375 Dock with Q96T88 Dock with Q9BUL5

Structure

/e3_file/ligand_db/generated/BDB056273/BDB056273.sdf

Basic Properties

Compound ID

E3L056273

Internal ID

BDB056273

Molecular formula

C23H32N4O2

Molecular weight

396.535000

Exact mass

396.252526

XLogP

1.8225

TPSA

55.8900

HBA / HBD

4 / 1

Rotatable bonds

Heavy atoms / rings

29 / 5

Activity summary

IC50 > 10000.00000000 nM
3 activity record(s) imported

InChIKey

MKARHKYZRAPRFF-UHFFFAOYSA-N

SMILES

O=C(c1ccc(C(=O)N2CC3(CCNC3)C2)cc1)N1CCC(N2CCCC2)CC1

Aliases

BDBM50440581 (preferred) [4-(2,7-Diazaspiro[3.4]octane-2-carbonyl)phenyl]-(4-pyrrolidin-1-ylpiperidin-1-yl)methanone (source_name) BDBM50440581 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
P29375	KDM5A;JARID1A;RBBP2;RBP2 Lysine-specific demethylase 5A	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50440581	medium ; target=Lysine-specific demethylase 5A
Q96T88	UHRF1;ICBP90;NP95;RNF106 E3 ubiquitin-protein ligase UHRF1	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50440581	medium ; target=E3 ubiquitin-protein ligase UHRF1
Q9BUL5	PHF23 PHD finger protein 23 (PDH-containing protein JUNE-1)	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50440581	medium ; target=PHD finger protein 23

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50440581	Open	-	10.1021/jm400919p PMID: 24040942
PubChem	CID73334479	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C(c1ccc(C(=O)N2CC3(CCNC3)C2)cc1)N1CCC(N2CCCC2)CC1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB056273/BDB056273.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB056273/BDB056273.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB056273/BDB056273.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB056273/BDB056273.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB056273/BDB056273.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
E3 ubiquitin-protein ligase UHRF1 Q96T88 E3 ligase component	BindingDB:BDBM50440581	IC50	>10000 nM	Low	DOI: 10.1021/jm400919p PMID: 24040942	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50440581	IC50	>10000 nM	Low	DOI: 10.1021/jm400919p PMID: 24040942	1
PHD finger protein 23 Q9BUL5 E3 ligase component	BindingDB:BDBM50440581	IC50	>10000 nM	Low	DOI: 10.1021/jm400919p PMID: 24040942	1