E3Docker 2.0

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Lenalidomide

E3L065888

Internal ID: LIG000458

MGDE3-ligand related Activity data available Local docking-ready structure

Dock with Q16531 Dock with Q96SW2

Structure

/e3_file/ligand_db/generated/LIG000458/LIG000458.sdf

Basic Properties

Compound ID

E3L065888

Internal ID

LIG000458

Molecular formula

C13H13N3O3

Molecular weight

259.265000

Exact mass

259.095691

XLogP

0.0298

TPSA

92.5000

HBA / HBD

4 / 2

Rotatable bonds

Heavy atoms / rings

19 / 3

Activity summary

IC50 unknown 89.00000000 nM
21 activity record(s) imported

InChIKey

GOTYRUGSSMKFNF-UHFFFAOYSA-N

SMILES

Nc1cccc2c1CN(C1CCC(=O)NC1=O)C2=O

Aliases

Lenalidomide (preferred) 1b(lena) (synonym) Lenalidomide (synonym) lenalidomide (synonym) 1b(lena) (source_name) lenalidomide (source_name) Lenalidomide (source_name) lenalidomide (source_name) S-Lenalidomide (source_name) BDBM65454 (source_id) e3_ligand:4 (source_id) e3_ligand:64 (source_id) MolGlueDB:828 (source_id) MolGlueDB:828 (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:BDBM65454	medium ; target=DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM65454	medium ; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:4	high ; deduplicated e3_ligand:4 into MolGlueDB:828; exact_duplicate; Tanimoto 1.0
Q96SW2	CRBN;AD-006 Protein cereblon	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:64	high ; deduplicated e3_ligand:64 into MolGlueDB:828; exact_duplicate_canonical; Tanimoto 1.0

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
MolGlueDB	MGDB828	Open	-
e3_ligand	4	Open	-	10.1038/nature13527
e3_ligand	64	Open	-	10.1038/nature13527
BindingDB	BDBM65454	Open	-	10.1038/leu.2012.119; 10.1021/acs.jmedchem.6b01921; 10.7270/Q261146J; 10.1021/acsmedchemlett.0c00214; 10.1021/acsmedchemlett.0c00440; 10.1021/acs.jmedchem.3c00851; 10.7270/Q20C51FJ; 10.7270/Q26978B1; 10.7270/Q23201MQ; 10.7270/Q2N58RXG; 10.7270/Q2V12923; 10.1021/acs.jmedchem.3c01186; 10.7270/Q2348R1H; 10.7270/Q2SX6JS8; 10.7270/Q21V5KJN PMID: 22552008; 28425720; 32550984; 33488967; 37902300; 39132814; 36970148; 37647546; 38321747; 37984298

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM65454	BDBM65454	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:4	lenalidomide	exact_full_inchikey	no_new_e3_ligand_compound_link_evidence_to_base	1.000000 chiral 1.000000	deduplicated into MolGlueDB:828; exact_duplicate; Tanimoto 1.0
e3_ligand:64	S-Lenalidomide	exact_full_inchikey	no_new_e3_ligand_compound_link_evidence_to_base	1.000000 chiral 1.000000	deduplicated into MolGlueDB:828; exact_duplicate_canonical; Tanimoto 1.0

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	Nc1cccc2c1CN(C1CCC(=O)NC1=O)C2=O	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000458/LIG000458.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000458/LIG000458.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000458/LIG000458.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000458/LIG000458.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000458/LIG000458.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM65454	IC50	1500 nM	Low	DOI: 10.1021/acs.jmedchem.6b01921 PMID: 28425720	2 source records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM65454	IC50	3000 nM	Low	DOI: 10.1038/leu.2012.119 PMID: 22552008	2 source records
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	3600 nM	Low	DOI: 10.1021/acs.jmedchem.3c01186 PMID: 37647546	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	5190 nM	Low	DOI: 10.7270/Q261146J	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	2380 nM	Low	DOI: 10.7270/Q26978B1	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	2250 nM	Low	DOI: 10.7270/Q23201MQ	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	2000 nM	Low	DOI: 10.1038/leu.2012.119 PMID: 22552008	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	3100 nM	Low	DOI: 10.7270/Q2N58RXG	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	19000 nM	Low	DOI: 10.1021/acs.jmedchem.3c00851 PMID: 37902300	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	390 nM	Moderate	DOI: 10.7270/Q2V12923 PMID: 36970148	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	37800 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	IC50	89 nM	High	DOI: 10.7270/Q2348R1H PMID: 38321747	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Kd	178 nM	Moderate	DOI: 10.7270/Q21V5KJN PMID: 37984298	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Kd	100 nM	High	DOI: 10.7270/Q2SX6JS8	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Ki	16300 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Ki	800 nM	Moderate	DOI: 10.7270/Q20C51FJ PMID: 39132814	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Ki	1490 nM	Low	DOI: 10.1021/acsmedchemlett.0c00214 PMID: 32550984	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Ki	6400 nM	Low	DOI: 10.1021/acs.jmedchem.3c00851 PMID: 37902300	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65454	Ki	1490 nM	Low	DOI: 10.7270/Q261146J	1