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Pomalidomide

E3L067001

Internal ID: LIG001571

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

Dock with Q16531 Dock with Q96SW2

Structure

/e3_file/ligand_db/generated/LIG001571/LIG001571.sdf

Basic Properties

Compound ID

E3L067001

Internal ID

LIG001571

Molecular formula

C13H11N3O4

Molecular weight

273.248000

Exact mass

273.074956

XLogP

-0.3300

TPSA

109.5700

HBA / HBD

5 / 2

Rotatable bonds

Heavy atoms / rings

20 / 3

Activity summary

IC50 unknown 63.00000000 nM
17 activity record(s) imported

InChIKey

UVSMNLNDYGZFPF-UHFFFAOYSA-N

SMILES

Nc1cccc2c1C(=O)N(C1CCC(=O)NC1=O)C2=O

Aliases

Pomalidomide (preferred) 1c(poma) (synonym) 3(poma) (synonym) 4-NH2-Thal(Pomalidomide) (synonym) Pomalidomide (synonym) pomalidomide (synonym) 1c(poma) (source_name) 3(poma) (source_name) 4-NH2-Thal(Pomalidomide) (source_name) pomalidomide (source_name) Pomalidomide (source_name) pomalidomide (source_name) BDBM65456 (source_id) e3_ligand:2 (source_id) MolGlueDB:825 (source_id) MolGlueDB:825 (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:BDBM65456	medium ; target=DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM65456	medium ; target=Protein cereblon; DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:2	high ; deduplicated e3_ligand:2 into MolGlueDB:825; exact_duplicate; Tanimoto 1.0

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
MolGlueDB	MGDB825	Open	-
e3_ligand	2	Open	-	10.1038/nature13527
BindingDB	BDBM65456	Open	-	10.1038/leu.2012.119; 10.1021/acs.jmedchem.6b01921; 10.7270/Q2G44TFM; 10.1021/acsmedchemlett.0c00440; 10.1021/acs.jmedchem.3c00851; 10.7270/Q2N58RXG; 10.7270/Q2V12923; 10.1021/acs.jmedchem.3c00176; 10.7270/Q2XD15TB; 10.7270/Q2QF8ZC5; 10.7270/Q21V5KJN PMID: 22552008; 28425720; 33488967; 37902300; 36970148; 37195170; 37984298

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM65456	BDBM65456	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:2	pomalidomide	exact_full_inchikey	no_new_e3_ligand_compound_link_evidence_to_base	1.000000 chiral 1.000000	deduplicated into MolGlueDB:825; exact_duplicate; Tanimoto 1.0

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	Nc1cccc2c1C(=O)N(C1CCC(=O)NC1=O)C2=O	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG001571/LIG001571.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG001571/LIG001571.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG001571/LIG001571.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG001571/LIG001571.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG001571/LIG001571.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM65456	IC50	63 nM	High	DOI: 10.7270/Q2G44TFM	2 source records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM65456	IC50	1200 nM	Low	DOI: 10.1021/acs.jmedchem.6b01921 PMID: 28425720	2 source records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM65456	IC50	3000 nM	Low	DOI: 10.1038/leu.2012.119 PMID: 22552008	2 source records
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	IC50	1300 nM	Low	DOI: 10.7270/Q2N58RXG	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	IC50	83 nM	High	DOI: 10.1021/acs.jmedchem.3c00176 PMID: 37195170	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	IC50	25800 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	IC50	13000 nM	Low	DOI: 10.1021/acs.jmedchem.3c00851 PMID: 37902300	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	IC50	739 nM	Moderate	DOI: 10.7270/Q2V12923 PMID: 36970148	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	IC50	2000 nM	Low	DOI: 10.1038/leu.2012.119 PMID: 22552008	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	Kd	5100 nM	Low	DOI: 10.7270/Q2XD15TB	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	Kd	>1000 nM	Moderate	DOI: 10.7270/Q2QF8ZC5	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	Kd	157 nM	Moderate	DOI: 10.7270/Q21V5KJN PMID: 37984298	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	Ki	10000 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65456	Ki	3300 nM	Low	DOI: 10.1021/acs.jmedchem.3c00851 PMID: 37902300	1