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BDBM50652775

E3L065420
Internal ID: BDB065420
Activity data available Local docking-ready structure
Dock with P29375 Dock with P41229 Dock with Q8NHM5
Structure
/e3_file/ligand_db/generated/BDB065420/BDB065420.sdf
Basic Properties
Compound ID
E3L065420
Internal ID
BDB065420
Molecular formula
C22H23N5O2
Molecular weight
389.459000
Exact mass
389.185175
XLogP
3.0304
TPSA
91.2400
HBA / HBD
6 / 2
Rotatable bonds
6
Heavy atoms / rings
29 / 4
Activity summary
IC50 > 2.00000000 nM
3 activity record(s) imported
InChIKey
LJIFOCRGDDQFJF-UHFFFAOYSA-N
SMILES
O=C(O)CCNc1cc(N2CCc3ccccc3CC2)nc(-c2cccnc2)n1
Aliases
BDBM50652775 (preferred) 3-[[2-(3-Pyridinyl)-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)-4-pyrimidinyl]amino]propanoic acid (source_name) BDBM50652775 (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:BDBM50652775 medium
; target=Lysine-specific demethylase 5A
P41229 KDM5C;DXS1272E;JARID1C;SMCX;XE169
Lysine-specific demethylase 5C		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50652775 medium
; target=Lysine-specific demethylase 5C
Q8NHM5 KDM2B;CXXC2;FBL10;FBXL10;JHDM1B;NDY1;PCCX2
Lysine-specific demethylase 2B		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50652775 medium
; target=Lysine-specific demethylase 2B
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM50652775 Open - 10.7270/Q2C2525P PMID: 25279926
PubChem CID73010924 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C(O)CCNc1cc(N2CCc3ccccc3CC2)nc(-c2cccnc2)n1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB065420/BDB065420.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB065420/BDB065420.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB065420/BDB065420.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB065420/BDB065420.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB065420/BDB065420.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
Lysine-specific demethylase 2B
Q8NHM5
E3 ligase component 		BindingDB:BDBM50652775 IC50 8.3 nM Very high DOI: 10.7270/Q2C2525P
PMID: 25279926 		1
Lysine-specific demethylase 5A
P29375
E3 ligase component 		BindingDB:BDBM50652775 IC50 >2 nM Uncertain DOI: 10.7270/Q2C2525P
PMID: 25279926 		1
Lysine-specific demethylase 5C
P41229
E3 ligase component 		BindingDB:BDBM50652775 IC50 >7.5 nM Uncertain DOI: 10.7270/Q2C2525P
PMID: 25279926 		1