E3Docker 2.0

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Thalidomide

E3L066929

Internal ID: LIG001499

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

Dock with Q16531 Dock with Q96SW2

Structure

/e3_file/ligand_db/generated/LIG001499/LIG001499.sdf

Basic Properties

Compound ID

E3L066929

Internal ID

LIG001499

Molecular formula

C13H10N2O4

Molecular weight

258.233000

Exact mass

258.064057

XLogP

0.0878

TPSA

83.5500

HBA / HBD

4 / 1

Rotatable bonds

Heavy atoms / rings

19 / 3

Activity summary

Kd unknown 250.00000000 nM
21 activity record(s) imported

InChIKey

UEJJHQNACJXSKW-UHFFFAOYSA-N

SMILES

O=C1CCC(N2C(=O)c3ccccc3C2=O)C(=O)N1

Aliases

Thalidomide (preferred) 1a(thal) (synonym) Thalidomide (synonym) 1a(thal) (source_name) Thalidomide (source_name) Thalidomide (source_name) BDBM50070114 (source_id) e3_ligand:3 (source_id) MolGlueDB:1041 (source_id) MolGlueDB:1041 (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:BDBM50070114	medium ; target=DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50070114	medium ; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:3	high ; deduplicated e3_ligand:3 into MolGlueDB:1041; exact_duplicate; Tanimoto 1.0

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
MolGlueDB	MGDB1041	Open	-
e3_ligand	3	Open	-	10.1038/nature13527
BindingDB	BDBM50070114	Open	-	10.1038/leu.2012.119; 10.7270/Q2G44TFM; 10.1021/acs.jmedchem.5b01735; 10.1021/acsmedchemlett.0c00440; 10.1021/acs.jmedchem.2c01882; 10.1016/j.ejmech.2022.114990; 10.1021/acs.jmedchem.3c01264; 10.7270/Q2PC3713; 10.7270/Q20K2F7R; 10.7270/Q20C51FJ; 10.7270/Q2V12923; 10.1021/acs.jmedchem.3c01186; 10.7270/Q2NV9PV1; 10.7270/Q2QF8ZC5; 10.7270/Q21V5KJN; 10.7270/Q2RB7999 PMID: 22552008; 26730808; 33488967; 36821822; 36476642; 37683104; 38552426; 38917956; 39132814; 36970148; 37647546; 38829718; 37984298; 37210838

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM50070114	BDBM50070114	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:3	Thalidomide	exact_full_inchikey	no_new_e3_ligand_compound_link_evidence_to_base	1.000000 chiral 1.000000	deduplicated into MolGlueDB:1041; exact_duplicate; Tanimoto 1.0

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C1CCC(N2C(=O)c3ccccc3C2=O)C(=O)N1	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG001499/LIG001499.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG001499/LIG001499.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG001499/LIG001499.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG001499/LIG001499.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG001499/LIG001499.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM50070114	IC50	301 nM	Moderate	DOI: 10.7270/Q2G44TFM	2 source records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM50070114	IC50	268 nM	Moderate	DOI: 10.7270/Q2G44TFM	2 source records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM50070114	IC50	30000 nM	Low	DOI: 10.1038/leu.2012.119 PMID: 22552008	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	IC50	22900 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	IC50	2900 nM	Low	DOI: 10.1021/acs.jmedchem.3c01186 PMID: 37647546	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	IC50	29900 nM	Low	DOI: 10.1021/acs.jmedchem.5b01735 PMID: 26730808	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	IC50	1490 nM	Low	DOI: 10.7270/Q2V12923 PMID: 36970148	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	IC50	2700 nM	Low	DOI: 10.7270/Q2NV9PV1 PMID: 38829718	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Kd	250 nM	Moderate	DOI: 10.7270/Q2RB7999 PMID: 37210838	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Kd	250 nM	Moderate	DOI: 10.7270/Q21V5KJN PMID: 37984298	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Kd	>1000 nM	Moderate	DOI: 10.7270/Q2QF8ZC5	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	22700 nM	Low	DOI: 10.1021/acs.jmedchem.5b01735 PMID: 26730808	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	8500 nM	Low	DOI: 10.7270/Q2PC3713 PMID: 38552426	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	1800 nM	Low	DOI: 10.1021/acs.jmedchem.3c01264 PMID: 37683104	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	1800 nM	Low	DOI: 10.7270/Q20C51FJ PMID: 39132814	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	4400 nM	Low	DOI: 10.1021/acs.jmedchem.2c01882 PMID: 36821822	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	8510 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	8550 nM	Low	DOI: 10.7270/Q20K2F7R PMID: 38917956	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50070114	Ki	8500 nM	Low	DOI: 10.1016/j.ejmech.2022.114990 PMID: 36476642	1