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5-NH2-EM12

E3L067171
Internal ID: LIG001741
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/LIG001741/LIG001741.sdf
Basic Properties
Compound ID
E3L067171
Internal ID
LIG001741
Molecular formula
C13H13N3O3
Molecular weight
259.265000
Exact mass
259.095691
XLogP
0.0298
TPSA
92.5000
HBA / HBD
4 / 2
Rotatable bonds
1
Heavy atoms / rings
19 / 3
Activity summary
IC50 unknown 382.00000000 nM
3 activity record(s) imported
InChIKey
WLUIQUZGNPAKRL-UHFFFAOYSA-N
SMILES
Nc1ccc2c(c1)CN(C1CCC(=O)NC1=O)C2=O
Aliases
5-NH2-EM12 (preferred) Lenalidomide (source_name) BDBM50614100 (source_id) e3_ligand:137 (source_id) MolGlueDB:810 (source_id)
E3 Relation
E3 UniProt Gene / protein Relation type Ligand role Direct Functional Docking Source Evidence
Q16531 DDB1;XAP1
DNA damage-binding protein 1		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50614100 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50614100 medium
; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 direct_binder e3_ligand Yes Yes medium e3_ligand:137 high
; deduplicated e3_ligand:137 into MolGlueDB:810; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB810 Open -
e3_ligand 137 Open - 10.1038/nature13527
BindingDB BDBM50614100 Open - 10.7270/Q2FN1BRK; 10.7270/Q2V12923 PMID: 36970148
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM50614100 BDBM50614100 exact_full_inchikey no_new_bindingdb_compound_link_evidence_to_base 1.000000
chiral 1.000000 		Exact structure already exists in E3/MolGlue base library
e3_ligand:137 Lenalidomide exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:810; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Nc1ccc2c(c1)CN(C1CCC(=O)NC1=O)C2=O keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001741/LIG001741.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001741/LIG001741.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001741/LIG001741.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001741/LIG001741.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001741/LIG001741.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM50614100 Kd <10000 nM Uncertain DOI: 10.7270/Q2FN1BRK 2 source records
Protein cereblon
Q96SW2
E3 ligase component 		BindingDB:BDBM50614100 IC50 382 nM Moderate DOI: 10.7270/Q2V12923
PMID: 36970148 		1