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2

E3L066432
Internal ID: LIG001002
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with P40337 Dock with Q15369
Structure
/e3_file/ligand_db/generated/LIG001002/LIG001002.sdf
Basic Properties
Compound ID
E3L066432
Internal ID
LIG001002
Molecular formula
C27H33N5O4S
Molecular weight
523.659000
Exact mass
523.225326
XLogP
2.5312
TPSA
135.4200
HBA / HBD
7 / 3
Rotatable bonds
7
Heavy atoms / rings
37 / 4
Activity summary
Kd unknown 52.00000000 nM
14 activity record(s) imported
InChIKey
NDVQUNZCNAMROD-RZUBCFFCSA-N
SMILES
Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)[C@@H](NC(=O)C2(C#N)CC2)C(C)(C)C)cc1
Aliases
2 (preferred) VH298 (source_name) BDBM50459944 (source_id) e3_ligand:13 (source_id) MolGlueDB:272 (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:BDBM50459944 medium
; target=von Hippel-Lindau disease tumor suppressor
P40337 VHL
von Hippel-Lindau disease tumor suppressor		 direct_binder e3_ligand Yes Yes medium e3_ligand:13 high
; deduplicated e3_ligand:13 into MolGlueDB:272; exact_duplicate; Tanimoto 1.0
Q15369 ELOC;TCEB1
Elongin-C		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM50459944 medium
; target=Elongin-C
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB272 Open -
e3_ligand 13 Open - 10.1038/ncomms13312
BindingDB BDBM50459944 Open - 10.1021/acs.jmedchem.9b01451; 10.1021/acs.jmedchem.3c00434; 10.1021/acs.jmedchem.8b01596; 10.1021/acsmedchemlett.0c00265; 10.1016/j.bmc.2023.117334; 10.7270/Q21G0RV2; 10.1021/acs.jmedchem.7b00675 PMID: 32142281; 37708384; 30682255; 32939229; 37224698; 38199162; 28853884
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM50459944 BDBM50459944 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:13 VH298 exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:272; exact_duplicate; Tanimoto 1.0
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready Cc1ncsc1-c1ccc(CNC(=O)[C@@H]2C[C@@H](O)CN2C(=O)[C@@H](NC(=O)C2(C#N)CC2)C(C)(C)C)cc1 keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG001002/LIG001002.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG001002/LIG001002.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG001002/LIG001002.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG001002/LIG001002.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG001002/LIG001002.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 80 nM High DOI: 10.1021/acs.jmedchem.3c00434
PMID: 37708384 		1
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 80 nM High DOI: 10.1021/acs.jmedchem.7b00675
PMID: 28853884 		1
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 129 nM Moderate DOI: 10.1021/acs.jmedchem.3c00434
PMID: 37708384 		1
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 90 nM High DOI: 10.1021/acs.jmedchem.3c00434
PMID: 37708384 		1
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 99 nM High DOI: 10.1021/acs.jmedchem.7b00675
PMID: 28853884 		1
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 90 nM High DOI: 10.1021/acs.jmedchem.7b00675
PMID: 28853884 		1
Elongin-C
Q15369
E3 ligase component 		BindingDB:BDBM50459944 Kd 52 nM High DOI: 10.1021/acs.jmedchem.7b00675
PMID: 28853884 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 IC50 576 nM Moderate DOI: 10.1021/acs.jmedchem.3c00434
PMID: 37708384 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 IC50 750 nM Moderate DOI: 10.1021/acs.jmedchem.3c00434
PMID: 37708384 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 IC50 88 nM High DOI: 10.1021/acs.jmedchem.9b01451
PMID: 32142281 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 Kd 58 nM High DOI: 10.1021/acsmedchemlett.0c00265
PMID: 32939229 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 Kd 90 nM High DOI: 10.1021/acs.jmedchem.8b01596
PMID: 30682255 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 Kd 90 nM High DOI: 10.1016/j.bmc.2023.117334
PMID: 37224698 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50459944 Kd 129 nM Moderate DOI: 10.7270/Q21G0RV2
PMID: 38199162 		1