E3Docker 2.0

Gsk-J1

E3L003220

Internal ID: BDB003220

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB003220/BDB003220.sdf

Basic Properties

Compound ID

E3L003220

Internal ID

BDB003220

Molecular formula

C22H23N5O2

Molecular weight

389.459000

Exact mass

389.185175

XLogP

3.0304

TPSA

91.2400

HBA / HBD

6 / 2

Rotatable bonds

Heavy atoms / rings

29 / 4

Activity summary

IC50 unknown 1200.00000000 nM
9 activity record(s) imported

InChIKey

AVZCPICCWKMZDT-UHFFFAOYSA-N

SMILES

O=C(O)CCNc1cc(N2CCc3ccccc3CC2)nc(-c2ccccn2)n1

Aliases

BDBM60875 (preferred) Gsk-J1 (source_name) BDBM60875 (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:BDBM60875	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM60875	medium ; target=Lysine-specific demethylase 5C
Q8NHM5	KDM2B;CXXC2;FBL10;FBXL10;JHDM1B;NDY1;PCCX2 Lysine-specific demethylase 2B	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM60875	medium ; target=Lysine-specific demethylase 2B
Q9BY66	KDM5D;HY;HYA;JARID1D;KIAA0234;SMCY Lysine-specific demethylase 5D	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM60875	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM60875	Open	-	10.1038/nchembio.2085; 10.1021/acs.jmedchem.8b01219; 10.7270/Q2N01BRW; 10.1038/nchembio.2087 PMID: 27214401; 30392349; 34555614; 27214403
PubChem	CID56963315	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C(O)CCNc1cc(N2CCc3ccccc3CC2)nc(-c2ccccn2)n1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB003220/BDB003220.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB003220/BDB003220.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB003220/BDB003220.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB003220/BDB003220.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB003220/BDB003220.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 2B Q8NHM5 E3 ligase component	BindingDB:BDBM60875	IC50	>25000 nM	Low	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM60875	IC50	2900 nM	Low	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM60875	IC50	3900 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM60875	IC50	6800 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM60875	IC50	110000 nM	Low	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM60875	Kd	12000 nM	Low	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM60875	IC50	1500 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM60875	IC50	1200 nM	Low	DOI: 10.1038/nchembio.2085 PMID: 27214401	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM60875	IC50	1500 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1