E3Docker 2.0

BDBM195612

E3L008102

Internal ID: BDB008102

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB008102/BDB008102.sdf

Basic Properties

Compound ID

E3L008102

Internal ID

BDB008102

Molecular formula

C17H13N5O2

Molecular weight

319.324000

Exact mass

319.106925

XLogP

2.3552

TPSA

85.6900

HBA / HBD

5 / 1

Rotatable bonds

Heavy atoms / rings

24 / 4

Activity summary

IC50 unknown 24.00000000 nM
7 activity record(s) imported

InChIKey

ZTYRLXUTLYBVHH-UHFFFAOYSA-N

SMILES

O=c1[nH]c(Oc2cnn(Cc3ccccc3)c2)nc2cnccc12

Aliases

BDBM195612 (preferred) 2-((1-Benzyl-1H-pyrazol-4-yl)oxy)pyrido[3,4-d]pyrimidin-4(3H)-one (source_name) BDBM195612 (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:BDBM195612	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM195612	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:BDBM195612	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM195612	Open	-	10.1038/nchembio.2087; 10.1021/acs.jmedchem.5b01538; 10.7270/Q2W95F76 PMID: 27214403; 26771203; 35838529
PubChem	CID135567128	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=c1[nH]c(Oc2cnn(Cc3ccccc3)c2)nc2cnccc12	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB008102/BDB008102.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB008102/BDB008102.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB008102/BDB008102.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB008102/BDB008102.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB008102/BDB008102.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM195612	IC50	24 nM	High	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195612	IC50	63 nM	High	DOI: 10.1021/acs.jmedchem.5b01538 PMID: 26771203	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195612	IC50	4000 nM	Low	DOI: 10.7270/Q2W95F76 PMID: 35838529	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195612	IC50	3981 nM	Low	DOI: 10.1021/acs.jmedchem.5b01538 PMID: 26771203	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195612	IC50	65 nM	High	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM195612	IC50	3980 nM	Low	DOI: 10.1021/acs.jmedchem.5b01538 PMID: 26771203	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM195612	IC50	77 nM	High	DOI: 10.1038/nchembio.2087 PMID: 27214403	1