E3Docker 2.0

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BDBM50440612

E3L056304

Internal ID: BDB056304

Activity data available Local docking-ready structure

Dock with P29375 Dock with Q96T88 Dock with Q9BUL5

Structure

/e3_file/ligand_db/generated/BDB056304/BDB056304.sdf

Basic Properties

Compound ID

E3L056304

Internal ID

BDB056304

Molecular formula

C33H44N4O2

Molecular weight

528.741000

Exact mass

528.346427

XLogP

4.6782

TPSA

47.1000

HBA / HBD

4 / 0

Rotatable bonds

Heavy atoms / rings

39 / 6

Activity summary

IC50 > 10000.00000000 nM
3 activity record(s) imported

InChIKey

IQFNTVZARNOVIR-UHFFFAOYSA-N

SMILES

O=C(c1ccc(C(=O)N2CCC(N3CCCC3)CC2)c(Cc2ccccc2)c1)N1CCC(N2CCCC2)CC1

Aliases

BDBM50440612 (preferred) [3-Benzyl-4-(4-pyrrolidin-1-ylpiperidine-1-carbonyl)phenyl]-(4-pyrrolidin-1-ylpiperidin-1-yl)methanone (source_name) BDBM50440612 (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:BDBM50440612	medium ; target=Lysine-specific demethylase 5A
Q96T88	UHRF1;ICBP90;NP95;RNF106 E3 ubiquitin-protein ligase UHRF1	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50440612	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:BDBM50440612	medium ; target=PHD finger protein 23

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50440612	Open	-	10.1021/jm400919p PMID: 24040942
PubChem	CID73333129	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C(c1ccc(C(=O)N2CCC(N3CCCC3)CC2)c(Cc2ccccc2)c1)N1CCC(N2CCCC2)CC1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB056304/BDB056304.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB056304/BDB056304.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB056304/BDB056304.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB056304/BDB056304.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB056304/BDB056304.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
E3 ubiquitin-protein ligase UHRF1 Q96T88 E3 ligase component	BindingDB:BDBM50440612	IC50	>10000 nM	Low	DOI: 10.1021/jm400919p PMID: 24040942	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50440612	IC50	>10000 nM	Low	DOI: 10.1021/jm400919p PMID: 24040942	1
PHD finger protein 23 Q9BUL5 E3 ligase component	BindingDB:BDBM50440612	IC50	>10000 nM	Low	DOI: 10.1021/jm400919p PMID: 24040942	1