E3Docker 2.0

Kdoam-28

E3L010304

Internal ID: BDB010304

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB010304/BDB010304.sdf

Basic Properties

Compound ID

E3L010304

Internal ID

BDB010304

Molecular formula

C17H29N5O2

Molecular weight

335.452000

Exact mass

335.232125

XLogP

0.3310

TPSA

77.5700

HBA / HBD

5 / 2

Rotatable bonds

Heavy atoms / rings

24 / 1

Activity summary

IC50 unknown 200.00000000 nM
5 activity record(s) imported

InChIKey

WXFDDWMINUVYFL-UHFFFAOYSA-N

SMILES

CCNC(=O)c1ccnc(CNCC(=O)N(CC)CCN(C)C)c1

Aliases

BDBM223318 (preferred) Kdoam-28 (source_name) BDBM223318 (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:BDBM223318	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM223318	medium ; target=Lysine-specific demethylase 5C
Q9BY66	KDM5D;HY;HYA;JARID1D;KIAA0234;SMCY Lysine-specific demethylase 5D	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM223318	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM223318	Open	-	10.1016/j.chembiol.2017.02.006; 10.7270/Q2N01BRW PMID: 28262558; 34555614
PubChem	CID126961672	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CCNC(=O)c1ccnc(CNCC(=O)N(CC)CCN(C)C)c1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010304/BDB010304.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010304/BDB010304.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB010304/BDB010304.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB010304/BDB010304.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB010304/BDB010304.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223318	IC50	6600 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM223318	IC50	300 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223318	IC50	6800 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM223318	IC50	200 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM223318	IC50	200 nM	Moderate	DOI: 10.1016/j.chembiol.2017.02.006 PMID: 28262558	1