E3Docker 2.0

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MG-277

E3L065508

Internal ID: LIG000078

MGD Activity data available Local docking-ready structure

Dock with Q00987 Dock with Q96SW2

Structure

/e3_file/ligand_db/generated/LIG000078/LIG000078.sdf

Basic Properties

Compound ID

E3L065508

Internal ID

LIG000078

Molecular formula

C41H42Cl2FN5O5

Molecular weight

774.721000

Exact mass

773.254703

XLogP

6.0711

TPSA

136.7100

HBA / HBD

6 / 4

Rotatable bonds

Heavy atoms / rings

54 / 8

Activity summary

IC50 unknown 2.00000000 nM
17 activity record(s) imported

InChIKey

BANRYGZZIMCKNA-OYGJEQPESA-N

SMILES

O=C1CCC(N2Cc3c(CCCCCNC(=O)[C@@H]4NC5(CCCCC5)[C@@]5(C(=O)Nc6cc(Cl)ccc65)[C@H]4c4cccc(Cl)c4F)cccc3C2=O)C(=O)N1

Aliases

MG-277 (preferred) BDBM50505628 (source_id) MolGlueDB:1121 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50505628	medium ; target=E3 ubiquitin-protein ligase Mdm2
Q96SW2	CRBN;AD-006 Protein cereblon	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50505628	medium ; target=Protein cereblon

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
MolGlueDB	MGDB1121	Open	-
BindingDB	BDBM50505628	Open	-	10.1021/acs.jmedchem.9b00846 PMID: 31560543

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM50505628	BDBM50505628	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=C1CCC(N2Cc3c(CCCCCNC(=O)[C@@H]4NC5(CCCCC5)[C@@]5(C(=O)Nc6cc(Cl)ccc65)[C@H]4c4cccc(Cl)c4F)cccc3C2=O)C(=O)N1	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000078/LIG000078.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000078/LIG000078.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000078/LIG000078.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000078/LIG000078.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000078/LIG000078.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50505628	IC50	68 nM	High	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	2072 nM	Low	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	982 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	623 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	2138 nM	Low	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	32 nM	High	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	29 nM	High	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	496 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	400 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	2 nM	Very high	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	419 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	3.1 nM	Very high	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	1372 nM	Low	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	964 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	168 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	96 nM	High	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1
Protein cereblon Q96SW2 E3 ligase component	BindingDB:BDBM50505628	IC50	211 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00846 PMID: 31560543	1