E3Docker 2.0

< Back to small molecule database

BDBM553008

E3L025673

Internal ID: BDB025673

Activity data available Local docking-ready structure

Dock with P61964 Dock with Q03164 Dock with Q15291 Dock with Q969U6

Structure

/e3_file/ligand_db/generated/BDB025673/BDB025673.sdf

Basic Properties

Compound ID

E3L025673

Internal ID

BDB025673

Molecular formula

C28H32F3N7O3

Molecular weight

571.604000

Exact mass

571.251873

XLogP

3.4684

TPSA

106.6900

HBA / HBD

8 / 2

Rotatable bonds

Heavy atoms / rings

41 / 5

Activity summary

Kd unknown 3.50000000 nM
6 activity record(s) imported

InChIKey

HLVBKFBJGZIHHT-HDICACEKSA-N

SMILES

C[C@@H]1CN(c2ccc(-c3cnc(N4CCOCC4)nc3)cc2NC(=O)c2c[nH]c(=O)cc2C(F)(F)F)C[C@H](C)N1C

Aliases

BDBM553008 (preferred) N-[5-(2-morpholin-4-ylpyrimidin-5-yl)-2-[(3S,5R)-3,4,5-trimethylpiperazin-1-yl]phenyl]-6-oxo-4-(trifluoromethyl)-1H-pyridine-3-carboxamide (source_name) BDBM553008 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
P61964	WDR5;BIG3 WD repeat-containing protein 5	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM553008	medium ; target=WD repeat-containing protein 5
Q03164	KMT2A;ALL1;CXXC7;HRX;HTRX;MLL;MLL1;TRX1 Histone-lysine N-methyltransferase 2A	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM553008	medium ; target=Histone-lysine N-methyltransferase 2A
Q15291	RBBP5;RBQ3 Retinoblastoma-binding protein 5	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM553008	medium ; target=Histone-lysine N-methyltransferase 2A
Q969U6	FBXW5;FBW5;PP3971 F-box/WD repeat-containing protein 5	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM553008	medium ; target=Histone-lysine N-methyltransferase 2A

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
BindingDB	BDBM553008	Open	-	10.7270/Q27W6GD6
PubChem	CID138542237	Open	-

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	C[C@@H]1CN(c2ccc(-c3cnc(N4CCOCC4)nc3)cc2NC(=O)c2c[nH]c(=O)cc2C(F)(F)F)C[C@H](C)N1C	keep_bindingdb_unique
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB025673/BDB025673.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB025673/BDB025673.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/BDB025673/BDB025673.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/BDB025673/BDB025673.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/BDB025673/BDB025673.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Histone-lysine N-methyltransferase 2A Q969U6 E3 ligase component	BindingDB:BDBM553008	IC50	1570 nM	Low	DOI: 10.7270/Q27W6GD6	1
Histone-lysine N-methyltransferase 2A Q15291 E3 ligase component	BindingDB:BDBM553008	IC50	1570 nM	Low	DOI: 10.7270/Q27W6GD6	1
Histone-lysine N-methyltransferase 2A Q03164 E3 ligase component	BindingDB:BDBM553008	IC50	1570 nM	Low	DOI: 10.7270/Q27W6GD6	1
Histone-lysine N-methyltransferase 2A Q03164 E3 ligase component	BindingDB:BDBM553008	Kd	3.5 nM	Very high	DOI: 10.7270/Q27W6GD6	1
WD repeat-containing protein 5 P61964 E3 ligase component	BindingDB:BDBM553008	Kd	3.5 nM	Very high	DOI: 10.7270/Q27W6GD6	2 source records