E3Docker 2.0

KDM5 inhibitor N71

E3L057397

Internal ID: BDB057397

Activity data available Local docking-ready structure

Dock with P29375

Structure

/e3_file/ligand_db/generated/BDB057397/BDB057397.sdf

Basic Properties

Compound ID

E3L057397

Internal ID

BDB057397

Molecular formula

C28H34N4O4S

Molecular weight

522.671000

Exact mass

522.230077

XLogP

4.6427

TPSA

95.0000

HBA / HBD

7 / 2

Rotatable bonds

Heavy atoms / rings

37 / 4

Activity summary

IC50 unknown 60.00000000 nM
10 activity record(s) imported

InChIKey

KIIDGZQVWULCMZ-JXMROGBWSA-N

SMILES

CN(C)C/C=C/C(=O)Nc1cccc(C(OCCN2CCCCC2)c2cc3nccc(C(=O)O)c3s2)c1

Aliases

BDBM50468050 (preferred) KDM5 inhibitor N71 (source_name) BDBM50468050 (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:BDBM50468050	medium ; target=Lysine-specific demethylase 5A

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50468050	Open	-	10.1021/acs.jmedchem.8b01219 PMID: 30392349
PubChem	CID137321153	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CN(C)C/C=C/C(=O)Nc1cccc(C(OCCN2CCCCC2)c2cc3nccc(C(=O)O)c3s2)c1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB057397/BDB057397.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB057397/BDB057397.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB057397/BDB057397.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB057397/BDB057397.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB057397/BDB057397.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	60 nM	High	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	180 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	2 source records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	110 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	2 source records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	100 nM	High	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	1240 nM	Low	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	360 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	IC50	220 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50468050	Ki	410 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b01219 PMID: 30392349	1