Structure of PDB 6boy Chain B Binding Site BS02

Receptor Information
>6boy Chain B (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIP
GQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYA
YREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLPST
MSAVQLESLNKCQIFPCSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAET
LMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPIDDVLRIQLLKIG
SAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGPMAAYVNP
HGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKF
TATKKDMSPQKFWGLTRSALLPTIP
Ligand information
Ligand IDRN6
InChIInChI=1S/C42H45ClN8O7S/c1-23-24(2)59-42-35(23)37(26-13-15-27(43)16-14-26)46-29(38-49-48-25(3)50(38)42)21-33(53)44-19-8-6-4-5-7-9-20-45-34(54)22-58-31-12-10-11-28-36(31)41(57)51(40(28)56)30-17-18-32(52)47-39(30)55/h10-16,29-30H,4-9,17-22H2,1-3H3,(H,44,53)(H,45,54)(H,47,52,55)/t29-,30-/m0/s1
InChIKeyJGQPZPLJOBHHBK-KYJUHHDHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1sc2n3c(C)nnc3[C@H](CC(=O)NCCCCCCCCNC(=O)COc4cccc5C(=O)N([C@H]6CCC(=O)NC6=O)C(=O)c45)N=C(c7ccc(Cl)cc7)c2c1C
ACDLabs 12.01n1c(C)n5c(n1)C(CC(NCCCCCCCCNC(=O)COc3cccc4C(=O)N(C2C(=O)NC(CC2)=O)C(c34)=O)=O)N=C(c6c5sc(C)c6C)c7ccc(cc7)Cl
OpenEye OEToolkits 2.0.6Cc1c(sc-2c1C(=NC(c3n2c(nn3)C)CC(=O)NCCCCCCCCNC(=O)COc4cccc5c4C(=O)N(C5=O)C6CCC(=O)NC6=O)c7ccc(cc7)Cl)C
CACTVS 3.385Cc1sc2n3c(C)nnc3[CH](CC(=O)NCCCCCCCCNC(=O)COc4cccc5C(=O)N([CH]6CCC(=O)NC6=O)C(=O)c45)N=C(c7ccc(Cl)cc7)c2c1C
OpenEye OEToolkits 2.0.6Cc1c(sc-2c1C(=N[C@H](c3n2c(nn3)C)CC(=O)NCCCCCCCCNC(=O)COc4cccc5c4C(=O)N(C5=O)[C@H]6CCC(=O)NC6=O)c7ccc(cc7)Cl)C
FormulaC42 H45 Cl N8 O7 S
Name
ChEMBL
DrugBank
ZINC
PDB chain6boy Chain B 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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PDB6boy Plasticity in binding confers selectivity in ligand-induced protein degradation.
Resolution3.33 Å
Binding residue
(original residue number in PDB)		N351 P352 H353 H378 S379 W380 W386 W400 F402
Binding residue
(residue number reindexed from 1)		N299 P300 H301 H326 S327 W328 W334 W348 F350
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.74,IC50~1.8uM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6boy, PDBe:6boy, PDBj:6boy
PDBsum6boy
PubMed29892083
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

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