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6

E3L066114
Internal ID: LIG000684
MGDE3-ligand related Activity data available Local docking-ready structure
Dock with P40337
Structure
/e3_file/ligand_db/generated/LIG000684/LIG000684.sdf
Basic Properties
Compound ID
E3L066114
Internal ID
LIG000684
Molecular formula
C25H34N4O4S
Molecular weight
486.638000
Exact mass
486.230077
XLogP
2.8083
TPSA
111.6300
HBA / HBD
6 / 3
Rotatable bonds
6
Heavy atoms / rings
34 / 3
Activity summary
Kd unknown 63.00000000 nM
5 activity record(s) imported
InChIKey
JAHUHEDUDMTTTF-COWZOJLOSA-N
SMILES
CC(=O)N[C@H](C(=O)N1C[C@H](O)C[C@H]1C(=O)N[C@@H](C)c1ccc(-c2scnc2C)cc1)C(C)(C)C
Aliases
6 (preferred) VHL-1 (source_name) BDBM50615684 (source_id) e3_ligand:15 (source_id) MolGlueDB:55 (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:BDBM50615684 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:15 high
; deduplicated e3_ligand:15 into MolGlueDB:55; exact_duplicate; Tanimoto 1.0
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
MolGlueDB MGDB55 Open -
e3_ligand 15 Open - 10.1021/acs.jmedchem.8b01572
BindingDB BDBM50615684 Open - 10.7270/Q2B85DF5; 10.7270/Q21G0RV2; 10.7270/Q23B64QB PMID: 30629437; 38199162; 38809766
BindingDB
Related evidence		 BDBM50637329 Open - 10.7270/Q21G0RV2 PMID: 38199162
same_connectivity_stereo_or_protonation_diff; Tanimoto 1.000000
Deduplication Evidence
Related source Related name Relationship Decision Tanimoto Note
BindingDB:BDBM50615684 BDBM50615684 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:15 VHL-1 exact_full_inchikey no_new_e3_ligand_compound_link_evidence_to_base 1.000000
chiral 1.000000 		deduplicated into MolGlueDB:55; exact_duplicate; Tanimoto 1.0
BindingDB:BDBM50637329 BDBM50637329 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant 1.000000
chiral 0.875000 		Morgan non-chiral Tanimoto >= 0.95; retained for SAR/stereo review
BindingDB:BDBM50637329 BDBM50637329 same_connectivity_stereo_or_protonation_diff keep_bindingdb_stereo_or_protonation_variant - Connectivity InChIKey matches, but full InChIKey/isomeric SMILES differs
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)N[C@@H](C)c1ccc(-c2scnc2C)cc1)C(C)(C)C keep_base
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/LIG000684/LIG000684.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/LIG000684/LIG000684.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/LIG000684/LIG000684.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/LIG000684/LIG000684.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/LIG000684/LIG000684.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50615684 IC50 164 nM Moderate DOI: 10.7270/Q2B85DF5
PMID: 30629437 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50615684 IC50 130 nM Moderate DOI: 10.7270/Q21G0RV2
PMID: 38199162 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50615684 Kd 63 nM High DOI: 10.7270/Q21G0RV2
PMID: 38199162 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50615684 Kd 180 nM Moderate DOI: 10.7270/Q23B64QB
PMID: 38809766 		1
von Hippel-Lindau disease tumor suppressor
P40337
E3 ligase component 		BindingDB:BDBM50615684 Kd 120 nM Moderate DOI: 10.7270/Q23B64QB
PMID: 38809766 		1