E3Docker 2.0

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Nutlin-3A

E3L065520

Internal ID: LIG000090

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

Dock with O15151 Dock with Q00987

Structure

/e3_file/ligand_db/generated/LIG000090/LIG000090.sdf

Basic Properties

Compound ID

E3L065520

Internal ID

LIG000090

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 6.40000000 nM
40 activity record(s) imported

InChIKey

BDUHCSBCVGXTJM-WUFINQPMSA-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-3A (preferred) BDBM50229787 (source_id) e3_ligand:46 (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:BDBM50229787	medium ; target=Protein Mdm4
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50229787	medium ; target=E3 ubiquitin-protein ligase Mdm2
Q00987	MDM2 E3 ubiquitin-protein ligase Mdm2	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:46	high MDM2

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
e3_ligand	46	Open	-
BindingDB	BDBM50229787	Open	-	10.7270/Q2DV1Q2X; 10.1021/acs.jmedchem.3c01815; 10.1021/acs.jmedchem.5b00810; 10.7270/Q2TF032P; 10.7270/Q2833X64; 10.1016/j.ejmech.2014.05.027; 10.1016/j.bmcl.2014.04.063; 10.1016/j.ejmech.2012.08.003; 10.1021/acs.jmedchem.8b00664; 10.1021/acs.jmedchem.5b01913; 10.1021/acsmedchemlett.9b00620; 10.7270/Q2V69PP3; 10.1016/j.bmcl.2014.02.055; 10.1021/jm501092z; 10.1016/j.bmcl.2015.06.014; 10.1016/j.bmcl.2011.01.004; 10.1021/jm1011929; 10.1038/nature06526; 10.1016/j.bmcl.2008.07.114; 10.1016/j.bmcl.2012.08.086; 10.1016/j.bmc.2011.12.016; 10.1016/j.bmc.2012.11.026; 10.1021/jm400293z; 10.1016/j.bmcl.2013.03.034; 10.1021/ml4000657; 10.1016/j.ejmech.2018.08.099; 10.1016/j.bmcl.2018.08.027; 10.1016/j.ejmech.2019.05.018; 10.1021/acs.jmedchem.9b01451; 10.1021/jm8002813 PMID: 34286973; 38062557; 26181851; 39185935; 35763424; 24852275; 24813735; 22940704; 30045621; 26982372; 32435424; 35420431; 24656661; 25396320; 26115576; 21277201; 21314128; 18075579; 18752944; 22995624; 22227462; 23477941; 23597064; 23541651; 24900694; 30199707; 30217415; 31100649; 32142281; 18680271

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM50229787	BDBM50229787	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/LIG000090/LIG000090.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000090/LIG000090.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000090/LIG000090.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000090/LIG000090.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000090/LIG000090.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	88 nM	High	DOI: 10.1021/acs.jmedchem.9b01451 PMID: 32142281	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1038/nature06526 PMID: 18075579	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	30000 nM	Low	DOI: 10.1016/j.ejmech.2019.05.018 PMID: 31100649	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	89 nM	High	DOI: 10.1021/jm400293z PMID: 23597064	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1016/j.bmc.2012.11.026 PMID: 23477941	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1016/j.ejmech.2018.08.099 PMID: 30199707	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	610 nM	Moderate	DOI: 10.1016/j.bmcl.2015.06.014 PMID: 26115576	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1021/acsmedchemlett.9b00620 PMID: 32435424	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	19 nM	High	DOI: 10.7270/Q2DV1Q2X PMID: 34286973	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	100 nM	High	DOI: 10.1016/j.bmcl.2013.03.034 PMID: 23541651	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	88 nM	High	DOI: 10.1021/ml4000657 PMID: 24900694	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1021/jm501092z PMID: 25396320	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	61 nM	High	DOI: 10.1021/jm1011929 PMID: 21314128	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1016/j.bmcl.2012.08.086 PMID: 22995624	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	70 nM	High	DOI: 10.1016/j.bmcl.2014.02.055 PMID: 24656661	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	18 nM	High	DOI: 10.1021/jm400293z PMID: 23597064	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	90 nM	High	DOI: 10.1016/j.bmc.2011.12.016 PMID: 22227462	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	600 nM	Moderate	DOI: 10.1016/j.bmcl.2011.01.004 PMID: 21277201	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	13600 nM	Low	DOI: 10.1016/j.bmcl.2008.07.114 PMID: 18752944	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	IC50	10 nM	Very high	DOI: 10.1016/j.bmcl.2018.08.027 PMID: 30217415	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Kd	35 nM	High	DOI: 10.1021/acs.jmedchem.5b01913 PMID: 26982372	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Kd	20 nM	High	DOI: 10.7270/Q2TF032P PMID: 39185935	2 source records
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Kd	700 nM	Moderate	DOI: 10.1021/jm8002813 PMID: 18680271	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	43 nM	High	DOI: 10.1021/acs.jmedchem.3c01815 PMID: 38062557	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	70000 nM	Low	DOI: 10.7270/Q2DV1Q2X PMID: 34286973	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	39 nM	High	DOI: 10.7270/Q2V69PP3 PMID: 35420431	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	6.4 nM	Very high	DOI: 10.1021/acs.jmedchem.5b00810 PMID: 26181851	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	121 nM	Moderate	DOI: 10.1016/j.ejmech.2012.08.003 PMID: 22940704	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	59 nM	High	DOI: 10.1021/acs.jmedchem.5b01913 PMID: 26982372	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	110 nM	Moderate	DOI: 10.1016/j.ejmech.2014.05.027 PMID: 24852275	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	140 nM	Moderate	DOI: 10.1021/acs.jmedchem.8b00664 PMID: 30045621	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	90 nM	High	DOI: 10.1016/j.bmcl.2014.04.063 PMID: 24813735	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	150 nM	Moderate	DOI: 10.7270/Q2833X64 PMID: 35763424	1
E3 ubiquitin-protein ligase Mdm2 Q00987 E3 ligase component	BindingDB:BDBM50229787	Ki	43 nM	High	DOI: 10.1021/acsmedchemlett.9b00620 PMID: 32435424	1
Protein Mdm4 O15151 E3 ligase component	BindingDB:BDBM50229787	IC50	4300 nM	Low	DOI: 10.1021/acs.jmedchem.5b00810 PMID: 26181851	1
Protein Mdm4 O15151 E3 ligase component	BindingDB:BDBM50229787	Kd	6500 nM	Low	DOI: 10.7270/Q2TF032P PMID: 39185935	2 source records
Protein Mdm4 O15151 E3 ligase component	BindingDB:BDBM50229787	Ki	69000 nM	Low	DOI: 10.7270/Q2DV1Q2X PMID: 34286973	1
Protein Mdm4 O15151 E3 ligase component	BindingDB:BDBM50229787	Ki	1599 nM	Low	DOI: 10.1021/acs.jmedchem.3c01815 PMID: 38062557	1