E3Docker 2.0

Nutlin-3

E3L065519

Internal ID: LIG000089

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

Structure

/e3_file/ligand_db/generated/LIG000089/LIG000089.sdf

Basic Properties

Compound ID

E3L065519

Internal ID

LIG000089

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

Ki unknown 30.00000000 nM
10 activity record(s) imported

InChIKey

BDUHCSBCVGXTJM-UHFFFAOYSA-N

SMILES

COc1ccc(C2=NC(c3ccc(Cl)cc3)C(c3ccc(Cl)cc3)N2C(=O)N2CCNC(=O)C2)c(OC(C)C)c1

Aliases

Nutlin-3 (preferred) BDBM31197 (source_id) e3_ligand:9 (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:BDBM31197	medium ; target=Protein Mdm4
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM31197	medium ; target=E3 ubiquitin-protein ligase Mdm2
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:9	high MDM2

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
e3_ligand	9	Open	-
BindingDB	BDBM31197	Open	-	10.1021/acs.jmedchem.9b00993; 10.1021/jm051122a; 10.1021/jm060023+; 10.1016/j.ejmech.2016.11.029; 10.1016/j.ejmech.2021.113359; 10.1021/acs.jmedchem.5b01767; 10.1016/j.bmcl.2012.08.086; 10.7270/Q2668JC4; 10.1016/j.ejmech.2019.05.018 PMID: 31971801; 16759082; 16789731; 27907876; 33725632; 27050782; 22995624; 36092144; 31100649

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM31197	BDBM31197	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=NC(c3ccc(Cl)cc3)C(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/LIG000089/LIG000089.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000089/LIG000089.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000089/LIG000089.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000089/LIG000089.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000089/LIG000089.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	IC50	180 nM	Moderate	DOI: 10.1016/j.bmcl.2012.08.086 PMID: 22995624	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	IC50	105 nM	Moderate	DOI: 10.1021/acs.jmedchem.5b01767 PMID: 27050782	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	IC50	600 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b00993 PMID: 31971801	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	Kd	240 nM	Moderate	DOI: 10.1016/j.ejmech.2019.05.018 PMID: 31100649	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	Kd	263 nM	Moderate	DOI: 10.7270/Q2668JC4 PMID: 36092144	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	Ki	36 nM	High	DOI: 10.1021/jm060023+ PMID: 16789731	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	Ki	30 nM	High	DOI: 10.1016/j.ejmech.2016.11.029 PMID: 27907876	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	Ki	36 nM	High	DOI: 10.1021/jm051122a PMID: 16759082	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM31197	Ki	280 nM	Moderate	DOI: 10.1016/j.ejmech.2021.113359 PMID: 33725632	1
Protein Mdm4 O15151 E3 ligase component	BindingDB:BDBM31197	IC50	>10000 nM	Low	DOI: 10.1021/acs.jmedchem.9b00993 PMID: 31971801	1