E3Docker 2.0

N-Oxalylglycine

E3L000837

Internal ID: BDB000837

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB000837/BDB000837.sdf

Basic Properties

Compound ID

E3L000837

Internal ID

BDB000837

Molecular formula

C4H5NO5

Molecular weight

147.086000

Exact mass

147.016772

XLogP

-1.7282

TPSA

103.7000

HBA / HBD

3 / 3

Rotatable bonds

Heavy atoms / rings

10 / 0

Activity summary

IC50 unknown 3500.00000000 nM
6 activity record(s) imported

InChIKey

BIMZLRFONYSTPT-UHFFFAOYSA-N

SMILES

O=C(O)CNC(=O)C(=O)O

Aliases

BDBM26106 (preferred) N-Oxalylglycine (source_name) BDBM26106 (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:BDBM26106	medium ; target=Lysine-specific demethylase 5A
P41229	KDM5C;DXS1272E;JARID1C;SMCX;XE169 Lysine-specific demethylase 5C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM26106	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:BDBM26106	medium ; target=Lysine-specific demethylase 5D

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM26106	Open	-	10.1021/acsmedchemlett.5b00083; 10.1021/jm400624b; 10.1038/nchembio.2087; 10.1039/C4MD00291A PMID: 26101571; 23964788; 27214403; 26682034
PubChem	CID3080614	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C(O)CNC(=O)C(=O)O	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB000837/BDB000837.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB000837/BDB000837.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB000837/BDB000837.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB000837/BDB000837.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB000837/BDB000837.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26106	IC50	6900 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26106	IC50	640000 nM	Low	DOI: 10.1021/jm400624b PMID: 23964788	1
Lysine-specific demethylase 5A P29375 E3 ligase component	BindingDB:BDBM26106	IC50	250000 nM	Low	DOI: 10.1021/acsmedchemlett.5b00083 PMID: 26101571	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM26106	IC50	3500 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1
Lysine-specific demethylase 5C P41229 E3 ligase component	BindingDB:BDBM26106	IC50	7943 nM	Low	DOI: 10.1039/C4MD00291A PMID: 26682034	1
Lysine-specific demethylase 5D Q9BY66 E3 ligase component	BindingDB:BDBM26106	IC50	5800 nM	Low	DOI: 10.1038/nchembio.2087 PMID: 27214403	1