E3Docker 2.0

Nutlin-3B

E3L065518

Internal ID: LIG000088

E3-ligand related Activity data available Local docking-ready structure

Structure

/e3_file/ligand_db/generated/LIG000088/LIG000088.sdf

Basic Properties

Compound ID

E3L065518

Internal ID

LIG000088

Molecular formula

C30H30Cl2N4O4

Molecular weight

581.500000

Exact mass

580.164411

XLogP

5.8858

TPSA

83.4700

HBA / HBD

5 / 1

Rotatable bonds

Heavy atoms / rings

40 / 5

Activity summary

IC50 unknown 108.00000000 nM
6 activity record(s) imported

InChIKey

BDUHCSBCVGXTJM-IZLXSDGUSA-N

SMILES

COc1ccc(C2=N[C@H](c3ccc(Cl)cc3)[C@H](c3ccc(Cl)cc3)N2C(=O)N2CCNC(=O)C2)c(OC(C)C)c1

Aliases

Nutlin-3B (preferred) BDBM50392532 (source_id) e3_ligand:37 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
O15151	MDM4;MDMX Protein Mdm4	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50392532	medium ; target=Protein Mdm4
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50392532	medium ; target=E3 ubiquitin-protein ligase Mdm2
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:37	high MDM2

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
e3_ligand	37	Open	-
BindingDB	BDBM50392532	Open	-	10.1021/acs.jmedchem.7b00912; 10.1016/j.bmcl.2019.04.037; 10.1016/j.ejmech.2023.115282; 10.1016/j.bmcl.2012.08.086; 10.1016/j.bmc.2017.07.049 PMID: 28921985; 31047751; 36989812; 22995624; 28797774

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM50392532	BDBM50392532	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	COc1ccc(C2=N[C@H](c3ccc(Cl)cc3)[C@H](c3ccc(Cl)cc3)N2C(=O)N2CCNC(=O)C2)c(OC(C)C)c1	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000088/LIG000088.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000088/LIG000088.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000088/LIG000088.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000088/LIG000088.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000088/LIG000088.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50392532	IC50	108 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00912 PMID: 28921985	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50392532	IC50	13600 nM	Low	DOI: 10.1016/j.bmcl.2012.08.086 PMID: 22995624	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50392532	Kd	150 nM	Moderate	DOI: 10.1016/j.bmc.2017.07.049 PMID: 28797774	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50392532	Ki	198 nM	Moderate	DOI: 10.1016/j.bmcl.2019.04.037 PMID: 31047751	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50392532	Ki	110 nM	Moderate	DOI: 10.1016/j.ejmech.2023.115282 PMID: 36989812	1
Protein Mdm4 O15151 E3 ligase component	BindingDB:BDBM50392532	IC50	>1000 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00912 PMID: 28921985	1