E3Docker 2.0

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CC-220

E3L066096

Internal ID: LIG000666

MGD Activity data available Local docking-ready structure

Dock with Q16531 Dock with Q96SW2

Structure

/e3_file/ligand_db/generated/LIG000666/LIG000666.sdf

Basic Properties

Compound ID

E3L066096

Internal ID

LIG000666

Molecular formula

C25H27N3O5

Molecular weight

449.507000

Exact mass

449.195071

XLogP

1.8588

TPSA

88.1800

HBA / HBD

6 / 1

Rotatable bonds

Heavy atoms / rings

33 / 5

Activity summary

IC50 unknown 13.00000000 nM
5 activity record(s) imported

InChIKey

IXZOHGPZAQLIBH-NRFANRHFSA-N

SMILES

O=C1CC[C@H](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1

Aliases

CC-220 (preferred) CC-220 (synonym) Iberdomide (synonym) CC-220 (source_name) Iberdomide (source_name) BDBM65497 (source_id) MolGlueDB:916 (source_id) MolGlueDB:916 (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:BDBM65497	medium ; target=DNA damage-binding protein 1
Q96SW2	CRBN;AD-006 Protein cereblon	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM65497	medium ; target=Protein cereblon; DNA damage-binding protein 1

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
MolGlueDB	MGDB916	Open	-
BindingDB	BDBM65497	Open	-	10.1021/acs.jmedchem.6b01921; 10.1021/acsmedchemlett.0c00440; 10.1039/d3md00652b PMID: 28425720; 33488967; 38389883

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM65497	BDBM65497	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

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	O=C1CC[C@H](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000666/LIG000666.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000666/LIG000666.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000666/LIG000666.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000666/LIG000666.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000666/LIG000666.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
DNA damage-binding protein 1 Q16531 E3 ligase component	BindingDB:BDBM65497	IC50	60 nM	High	DOI: 10.1021/acs.jmedchem.6b01921 PMID: 28425720	2 source records
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65497	IC50	13 nM	High	DOI: 10.1039/d3md00652b PMID: 38389883	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65497	IC50	16000 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM65497	Ki	4940 nM	Low	DOI: 10.1021/acsmedchemlett.0c00440 PMID: 33488967	1