E3Docker 2.0

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4

E3L065858

Internal ID: LIG000428

MGDE3-ligand related Activity data available Local docking-ready structure

Dock with P40337 Dock with P62877 Dock with Q13617 Dock with Q15369 Dock with Q15370

Structure

/e3_file/ligand_db/generated/LIG000428/LIG000428.sdf

Basic Properties

Compound ID

E3L065858

Internal ID

LIG000428

Molecular formula

C24H32N4O4S

Molecular weight

472.611000

Exact mass

472.214427

XLogP

2.2473

TPSA

111.6300

HBA / HBD

6 / 3

Rotatable bonds

Heavy atoms / rings

33 / 3

Activity summary

Kd unknown 107.00000000 nM
30 activity record(s) imported

InChIKey

GFVIEZBZIUKYOG-SVFBPWRDSA-N

SMILES

CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)NCc1ccc(-c2scnc2C)cc1)C(C)(C)C

Aliases

4 (preferred) VH032 (source_name) BDBM50099062 (source_id) e3_ligand:12 (source_id) MolGlueDB:56 (source_id)

E3 Relation

E3 UniProt	Gene / protein	Relation type	Ligand role	Direct	Functional	Docking	Source	Evidence
P40337	VHL von Hippel-Lindau disease tumor suppressor	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50099062	medium ; target=von Hippel-Lindau disease tumor suppressor; Cullin-2; Hypoxia-inducible factor 1-alpha
P40337	VHL von Hippel-Lindau disease tumor suppressor	direct_binder	e3_ligand	Yes	Yes	medium	e3_ligand:12	high ; deduplicated e3_ligand:12 into MolGlueDB:56; exact_duplicate; Tanimoto 1.0
P62877	RBX1;RNF75;ROC1 E3 ubiquitin-protein ligase RBX1	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50099062	medium ; target=Cullin-2
Q13617	CUL2 Cullin-2	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50099062	medium ; target=Cullin-2
Q15369	ELOC;TCEB1 Elongin-C	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50099062	medium ; target=Elongin-C; Hypoxia-inducible factor 1-alpha
Q15370	ELOB;TCEB2 Elongin-B	reported_binder	bindingdb_reported	Yes	No	low	BindingDB:BDBM50099062	medium ; target=Hypoxia-inducible factor 1-alpha

Sources and Literature

Source	Source ID	Source URL	Download URL	DOI / PMID
MolGlueDB	MGDB56	Open	-
e3_ligand	12	Open	-	10.1038/ncomms13312
BindingDB	BDBM50099062	Open	-	10.7270/Q2WD43MN; 10.1021/acs.jmedchem.9b01451; 10.7270/Q2B85DF5; 10.7270/Q25B077N; 10.1021/jm5011258; 10.1021/acs.jmedchem.1c01496; 10.7270/Q2M049PD; 10.1016/j.bmc.2023.117334; 10.7270/Q23B64QB; 10.7270/Q2B85DSN; 10.7270/Q20K2DC4; 10.1021/acs.jmedchem.7b00635; 10.1021/acs.jmedchem.7b00675 PMID: 32142281; 30629437; 38478885; 25166285; 34881891; 36206538; 37224698; 38809766; 38621319; 28692295; 28853884

Deduplication Evidence

Related source	Related name	Relationship	Decision	Tanimoto	Note
BindingDB:BDBM50099062	BDBM50099062	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
e3_ligand:12	VH032	exact_full_inchikey	no_new_e3_ligand_compound_link_evidence_to_base	1.000000 chiral 1.000000	deduplicated into MolGlueDB:56; exact_duplicate; Tanimoto 1.0

Structure Files

Kind	Format	Status	Docking use	File / link	Preparation note
canonical_2d	SMILES	raw	Docking-ready	CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)NCc1ccc(-c2scnc2C)cc1)C(C)(C)C	keep_base
generated_3d	SDF	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000428/LIG000428.sdf	Generated from canonical SMILES
generated_3d	MOL2	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000428/LIG000428.mol2	Generated from canonical SMILES
docking_ready	PDBQT	prepared	Docking-ready	public/e3_file/ligand_db/generated/LIG000428/LIG000428.pdbqt	Generated from canonical SMILES
image	PNG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000428/LIG000428.png	Generated from canonical SMILES
image	SVG	prepared	Reference	public/e3_file/ligand_db/generated/LIG000428/LIG000428.svg	Generated from canonical SMILES

Activity

Target	Source	Assay	Result	Potency	Literature	Records
Cullin-2 Q13617 E3 ligase component	BindingDB:BDBM50099062	IC50	2540 nM	Low	DOI: 10.7270/Q20K2DC4	1
Cullin-2 Q13617 E3 ligase component	BindingDB:BDBM50099062	IC50	696 nM	Moderate	DOI: 10.7270/Q20K2DC4	1
Cullin-2 P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	696 nM	Moderate	DOI: 10.7270/Q20K2DC4	1
Cullin-2 P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	1480 nM	Low	DOI: 10.7270/Q20K2DC4	1
Cullin-2 Q13617 E3 ligase component	BindingDB:BDBM50099062	IC50	1480 nM	Low	DOI: 10.7270/Q20K2DC4	1
Cullin-2 P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	2540 nM	Low	DOI: 10.7270/Q20K2DC4	1
Cullin-2 P62877 E3 ligase component	BindingDB:BDBM50099062	IC50	1480 nM	Low	DOI: 10.7270/Q20K2DC4	1
Cullin-2 P62877 E3 ligase component	BindingDB:BDBM50099062	IC50	2540 nM	Low	DOI: 10.7270/Q20K2DC4	1
Cullin-2 P62877 E3 ligase component	BindingDB:BDBM50099062	IC50	696 nM	Moderate	DOI: 10.7270/Q20K2DC4	1
Elongin-C Q15369 E3 ligase component	BindingDB:BDBM50099062	Kd	107 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00675 PMID: 28853884	1
Elongin-C Q15369 E3 ligase component	BindingDB:BDBM50099062	Kd	185 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00675 PMID: 28853884	1
Elongin-C Q15369 E3 ligase component	BindingDB:BDBM50099062	Kd	150 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00675 PMID: 28853884	1
Elongin-C Q15369 E3 ligase component	BindingDB:BDBM50099062	Kd	123 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00675 PMID: 28853884	1
Hypoxia-inducible factor 1-alpha Q15370 E3 ligase component	BindingDB:BDBM50099062	IC50	800 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00635 PMID: 28692295	1
Hypoxia-inducible factor 1-alpha P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	800 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00635 PMID: 28692295	1
Hypoxia-inducible factor 1-alpha Q15369 E3 ligase component	BindingDB:BDBM50099062	IC50	800 nM	Moderate	DOI: 10.1021/acs.jmedchem.7b00635 PMID: 28692295	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	2540 nM	Low	DOI: 10.7270/Q2WD43MN	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	1480 nM	Low	DOI: 10.7270/Q2WD43MN	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	185 nM	Moderate	DOI: 10.1021/acs.jmedchem.9b01451 PMID: 32142281	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	458 nM	Moderate	DOI: 10.7270/Q2B85DF5 PMID: 30629437	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	696 nM	Moderate	DOI: 10.7270/Q2WD43MN	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	IC50	500 nM	Moderate	DOI: 10.7270/Q25B077N PMID: 38478885	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	185 nM	Moderate	DOI: 10.1016/j.bmc.2023.117334 PMID: 37224698	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	185 nM	Moderate	DOI: 10.7270/Q2B85DSN PMID: 38621319	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	200 nM	Moderate	DOI: 10.7270/Q23B64QB PMID: 38809766	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	180 nM	Moderate	DOI: 10.7270/Q23B64QB PMID: 38809766	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	113 nM	Moderate	DOI: 10.1021/acs.jmedchem.1c01496 PMID: 34881891	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	120 nM	Moderate	DOI: 10.7270/Q2WD43MN	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	185 nM	Moderate	DOI: 10.7270/Q2M049PD PMID: 36206538	1
von Hippel-Lindau disease tumor suppressor P40337 E3 ligase component	BindingDB:BDBM50099062	Kd	185 nM	Moderate	DOI: 10.1021/jm5011258 PMID: 25166285	1