E3Docker 2.0

Adenosylhomocysteine

E3L043579

Internal ID: BDB043579

Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/BDB043579/BDB043579.sdf

Basic Properties

Compound ID

E3L043579

Internal ID

BDB043579

Molecular formula

C14H20N6O5S

Molecular weight

384.418000

Exact mass

384.121589

XLogP

-1.4371

TPSA

182.6300

HBA / HBD

10 / 5

Rotatable bonds

Heavy atoms / rings

26 / 3

Activity summary

IC50 unknown 560.00000000 nM
4 activity record(s) imported

InChIKey

ZJUKTBDSGOFHSH-WFMPWKQPSA-N

SMILES

Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)[C@@H](O)[C@H]1O

Aliases

BDBM50009672 (preferred) Adenosylhomocysteine (source_name) BDBM50009672 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
O96028	NSD2;KIAA1090;MMSET;TRX5;WHSC1 Histone-lysine N-methyltransferase NSD2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50009672	medium ; target=Histone-lysine N-methyltransferase NSD2
Q03164	KMT2A;ALL1;CXXC7;HRX;HTRX;MLL;MLL1;TRX1 Histone-lysine N-methyltransferase 2A	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50009672	medium ; target=Histone-lysine N-methyltransferase 2A
Q9BQA1	WDR77;MEP50;WD45;HKMT1069;Nbla10071 Methylosome protein WDR77	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50009672	medium ; target=Protein arginine N-methyltransferase 5

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM50009672	Open	-	10.1016/j.ejmech.2021.113592; 10.1016/j.bmcl.2015.02.017; 10.1016/j.bmcl.2018.03.087; 10.1016/j.bmcl.2018.10.026 PMID: 34147909; 25746813; 29628326; 30366617
PubChem	CID439155	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)[C@@H](O)[C@H]1O	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB043579/BDB043579.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB043579/BDB043579.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB043579/BDB043579.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB043579/BDB043579.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB043579/BDB043579.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Histone-lysine N-methyltransferase 2A Q03164 E3 ligase component	BindingDB:BDBM50009672	IC50	2300 nM	Low	DOI: 10.1016/j.bmcl.2015.02.017 PMID: 25746813	1
Histone-lysine N-methyltransferase NSD2 O96028 E3 ligase component	BindingDB:BDBM50009672	IC50	39100 nM	Low	DOI: 10.1016/j.ejmech.2021.113592 PMID: 34147909	1
Protein arginine N-methyltransferase 5 Q9BQA1 E3 ligase component	BindingDB:BDBM50009672	IC50	560 nM	Moderate	DOI: 10.1016/j.bmcl.2018.10.026 PMID: 30366617	1
Protein arginine N-methyltransferase 5 Q9BQA1 E3 ligase component	BindingDB:BDBM50009672	IC50	600 nM	Moderate	DOI: 10.1016/j.bmcl.2018.03.087 PMID: 29628326	1