E3Docker 2.0

2,4-Pyridinedicarboxylic acid

E3L000838

Internal ID: BDB000838

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB000838/BDB000838.sdf

Basic Properties

Compound ID

E3L000838

Internal ID

BDB000838

Molecular formula

C7H5NO4

Molecular weight

167.120000

Exact mass

167.021858

XLogP

0.4780

TPSA

87.4900

HBA / HBD

3 / 2

Rotatable bonds

Heavy atoms / rings

12 / 1

Activity summary

IC50 unknown 501.00000000 nM
7 activity record(s) imported

InChIKey

MJIVRKPEXXHNJT-UHFFFAOYSA-N

SMILES

O=C(O)c1ccnc(C(=O)O)c1

Aliases

BDBM26113 (preferred) 2,4-Pyridinedicarboxylic acid (source_name) BDBM26113 (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:BDBM26113	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM26113	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:BDBM26113	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM26113	Open	-	10.1021/acs.jmedchem.5b01527; 10.1021/jm400624b; 10.7270/Q2N01BRW; 10.1038/nchembio.2087; 10.1039/C4MD00291A PMID: 26699912; 23964788; 34555614; 27214403; 26682034
PubChem	CID10365	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C(O)c1ccnc(C(=O)O)c1	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB000838/BDB000838.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB000838/BDB000838.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB000838/BDB000838.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB000838/BDB000838.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB000838/BDB000838.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26113	IC50	760 nM	Moderate	DOI: 10.1021/acs.jmedchem.5b01527 PMID: 26699912	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26113	IC50	100000 nM	Low	DOI: 10.1021/jm400624b PMID: 23964788	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26113	IC50	1300 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26113	IC50	4920 nM	Low	DOI: 10.7270/Q2N01BRW PMID: 34555614	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM26113	IC50	2000 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM26113	IC50	501 nM	Moderate	DOI: 10.1039/C4MD00291A PMID: 26682034	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM26113	IC50	2500 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1