< Back to small molecule database

BDBM97100

E3L004322
Internal ID: BDB004322
Activity data available Local docking-ready structure
Dock with Q16531 Dock with Q96SW2
Structure
/e3_file/ligand_db/generated/BDB004322/BDB004322.sdf
Basic Properties
Compound ID
E3L004322
Internal ID
BDB004322
Molecular formula
C42H46N6O5
Molecular weight
714.867000
Exact mass
714.352969
XLogP
4.6689
TPSA
127.3400
HBA / HBD
9 / 3
Rotatable bonds
8
Heavy atoms / rings
53 / 8
Activity summary
IC50 > 5000.00000000 nM
2 activity record(s) imported
InChIKey
SAHKNDRITROFCC-KKNODEMTSA-N
SMILES
O=C1CCC(NC(=O)c2ccc(N3CCC(CN4CCN(c5ccc([C@H]6c7ccc(O)cc7OC[C@H]6c6ccccc6)cc5)CC4)CC3)cn2)C(=O)N1
Aliases
BDBM97100 (preferred) N-(2,6-dioxopiperidin-3-yl)-5-(4-((4-(4-((3R,4S)-7-hydroxy-3-phenylchroman-4-yl)phenyl)piperazin-1-yl)methyl)piperidin-1-yl)picolinamide (source_name) BDBM97100 (source_id)
E3 Relation
E3 UniProt Gene / protein Relation type Ligand role Direct Functional Docking Source Evidence
Q16531 DDB1;XAP1
DNA damage-binding protein 1		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM97100 medium
; target=DNA damage-binding protein 1
Q96SW2 CRBN;AD-006
Protein cereblon		 reported_binder bindingdb_reported Yes No low BindingDB:BDBM97100 medium
; target=DNA damage-binding protein 1
Sources and Literature
Source Source ID Source URL Download URL DOI / PMID
BindingDB BDBM97100 Open - 10.7270/Q22F7T7F
PubChem CID170728479 Open -
Structure Files
Kind Format Status Docking use File / link Preparation note
canonical_2d SMILES raw Docking-ready O=C1CCC(NC(=O)c2ccc(N3CCC(CN4CCN(c5ccc([C@H]6c7ccc(O)cc7OC[C@H]6c6ccccc6)cc5)CC4)CC3)cn2)C(=O)N1 keep_bindingdb_unique
generated_3d SDF prepared Docking-ready public/e3_file/ligand_db/generated/BDB004322/BDB004322.sdf Generated from canonical SMILES
generated_3d MOL2 prepared Docking-ready public/e3_file/ligand_db/generated/BDB004322/BDB004322.mol2 Generated from canonical SMILES
docking_ready PDBQT prepared Docking-ready public/e3_file/ligand_db/generated/BDB004322/BDB004322.pdbqt Generated from canonical SMILES
image PNG prepared Reference public/e3_file/ligand_db/generated/BDB004322/BDB004322.png Generated from canonical SMILES
image SVG prepared Reference public/e3_file/ligand_db/generated/BDB004322/BDB004322.svg Generated from canonical SMILES
Activity
Target Source Assay Result Potency Literature Records
DNA damage-binding protein 1
Q16531
E3 ligase component 		BindingDB:BDBM97100 IC50 >5000 nM Low DOI: 10.7270/Q22F7T7F 2 source records