E3Docker 2.0

Daminozide

E3L055029

Internal ID: BDB055029

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB055029/BDB055029.sdf

Basic Properties

Compound ID

E3L055029

Internal ID

BDB055029

Molecular formula

C6H12N2O3

Molecular weight

160.173000

Exact mass

160.084792

XLogP

-0.5560

TPSA

69.6400

HBA / HBD

3 / 2

Rotatable bonds

Heavy atoms / rings

11 / 0

Activity summary

IC50 unknown 2100.00000000 nM
3 activity record(s) imported

InChIKey

NOQGZXFMHARMLW-UHFFFAOYSA-N

SMILES

CN(C)NC(=O)CCC(=O)O

Aliases

BDBM50395076 (preferred) Daminozide (source_name) BDBM50395076 (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:BDBM50395076	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50395076	medium ; target=Lysine-specific demethylase 5C
Q6ZMT4	KDM7A;JHDM1D;KDM7;KIAA1718 Lysine-specific demethylase 7A	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50395076	medium ; target=Lysine-specific demethylase 7A

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50395076	Open	-	10.1021/jm400624b; 10.1021/jm300677j PMID: 23964788; 22724510
PubChem	CID15331	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CN(C)NC(=O)CCC(=O)O	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB055029/BDB055029.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB055029/BDB055029.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB055029/BDB055029.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB055029/BDB055029.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB055029/BDB055029.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM50395076	IC50	2200000 nM	Low	DOI: 10.1021/jm400624b PMID: 23964788	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM50395076	IC50	>100000 nM	Low	DOI: 10.1021/jm300677j PMID: 22724510	1
Lysine-specific demethylase 7A Q6ZMT4 E3 ligase component	BindingDB:BDBM50395076	IC50	2100 nM	Low	DOI: 10.1021/jm300677j PMID: 22724510	1