Structure of PDB 7u8f Chain A Binding Site BS03

Receptor Information
>7u8f Chain A (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQEVSMVRNLIQKDR
TFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRFKVL
ELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQ
CSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENL
KDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKC
TSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKACNL
NLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFWGLT
RSALLPTIPDTEDEISPDKVILCL
Ligand information
Ligand IDLWK
InChIInChI=1S/C25H27N3O3/c29-23-9-8-22(24(30)26-23)28-16-20-14-19(6-7-21(20)25(28)31)18-10-12-27(13-11-18)15-17-4-2-1-3-5-17/h1-7,14,18,22H,8-13,15-16H2,(H,26,29,30)/t22-/m0/s1
InChIKeyOMISHRJQMYQPMG-QFIPXVFZSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1NC(=O)CCC1N1Cc2cc(ccc2C1=O)C1CCN(Cc2ccccc2)CC1
OpenEye OEToolkits 2.0.7c1ccc(cc1)CN2CCC(CC2)c3ccc4c(c3)CN(C4=O)C5CCC(=O)NC5=O
CACTVS 3.385O=C1CC[CH](N2Cc3cc(ccc3C2=O)C4CCN(CC4)Cc5ccccc5)C(=O)N1
OpenEye OEToolkits 2.0.7c1ccc(cc1)CN2CCC(CC2)c3ccc4c(c3)CN(C4=O)[C@H]5CCC(=O)NC5=O
CACTVS 3.385O=C1CC[C@H](N2Cc3cc(ccc3C2=O)C4CCN(CC4)Cc5ccccc5)C(=O)N1
FormulaC25 H27 N3 O3
Name(3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
ChEMBL
DrugBank
ZINC
PDB chain7u8f Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7u8f Discovery and characterization of a selective IKZF2 glue degrader for cancer immunotherapy.
Resolution3.15 Å
Binding residue
(original residue number in PDB)		N351 P352 H353 E377 H378 W380 W386 W400 F402
Binding residue
(residue number reindexed from 1)		N283 P284 H285 E309 H310 W312 W318 W332 F334
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0044325 transmembrane transporter binding
GO:0046872 metal ion binding
Biological Process
GO:0016567 protein ubiquitination
GO:0030177 positive regulation of Wnt signaling pathway
GO:0031333 negative regulation of protein-containing complex assembly
GO:0031334 positive regulation of protein-containing complex assembly
GO:0034766 negative regulation of monoatomic ion transmembrane transport
GO:0035641 locomotory exploration behavior
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:1902607 negative regulation of large conductance calcium-activated potassium channel activity
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex
GO:0048471 perinuclear region of cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:7u8f, PDBe:7u8f, PDBj:7u8f
PDBsum7u8f
PubMed36863346
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

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