Structure of PDB 5v3o Chain C Binding Site BS01

Receptor Information
>5v3o Chain C (length=363) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
INFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQT
LPLQLFHPQEVSMVRNLIQKDRTFAVLAYSAQFGTTAEIYAYREEQDFGI
EIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESL
NKCQIFPSSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQL
REWDDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIM
NKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNPHGYVHETLTVYKA
CNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTATKKDMSPQKFW
GLTRSALLPTIPD
Ligand information
Ligand ID8W7
InChIInChI=1S/C25H27N3O5/c29-23-9-8-21(24(30)26-23)28-15-20-19(25(28)31)2-1-3-22(20)33-16-18-6-4-17(5-7-18)14-27-10-12-32-13-11-27/h1-7,21H,8-16H2,(H,26,29,30)/t21-/m0/s1
InChIKeyIXZOHGPZAQLIBH-NRFANRHFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1cc(c2c(c1)C(N(C2)C3C(NC(CC3)=O)=O)=O)OCc5ccc(CN4CCOCC4)cc5
OpenEye OEToolkits 2.0.6c1cc2c(c(c1)OCc3ccc(cc3)CN4CCOCC4)CN(C2=O)C5CCC(=O)NC5=O
CACTVS 3.385O=C1CC[CH](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1
OpenEye OEToolkits 2.0.6c1cc2c(c(c1)OCc3ccc(cc3)CN4CCOCC4)CN(C2=O)[C@H]5CCC(=O)NC5=O
CACTVS 3.385O=C1CC[C@H](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1
FormulaC25 H27 N3 O5
Name(3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
ChEMBLCHEMBL3989927
DrugBankDB12101
ZINCZINC000118417658
PDB chain5v3o Chain C Residue 501 [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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PDB5v3o A Cereblon Modulator (CC-220) with Improved Degradation of Ikaros and Aiolos.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		N351 P352 E377 H378 S379 W380 W386 W400 F402
Binding residue
(residue number reindexed from 1)		N286 P287 E312 H313 S314 W315 W321 W335 F337
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.22,IC50=60nM
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5v3o, PDBe:5v3o, PDBj:5v3o
PDBsum5v3o
PubMed28425720
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

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