Structure of PDB 8d7u Chain B Binding Site BS02

Receptor Information
>8d7u Chain B (length=384) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMIL
IPGQTLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEI
YAYREEQDFGIEIVKVKAIGRQRFKVLELRTQSDGIQQAKVQILPECVLP
STMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQKYQKRKFHCANLTSWP
RWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVAACLPID
DVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLS
LCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQC
KICASHIGWKFTATKKDMSPQKFWGLTRSALLPT
Ligand information
Ligand IDQFC
InChIInChI=1S/C32H30FN5O4/c33-26-16-23(17-34)8-9-27(26)37-14-12-36(13-15-37)18-21-4-6-22(7-5-21)20-42-29-3-1-2-24-25(29)19-38(32(24)41)28-10-11-30(39)35-31(28)40/h1-9,16,28H,10-15,18-20H2,(H,35,39,40)/t28-/m0/s1
InChIKeyYTINZZFBHWSAGL-NDEPHWFRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1cc(ccc1N2CCN(CC2)Cc3ccc(COc4cccc5C(=O)N(Cc45)[C@H]6CCC(=O)NC6=O)cc3)C#N
OpenEye OEToolkits 2.0.7c1cc2c(c(c1)OCc3ccc(cc3)CN4CCN(CC4)c5ccc(cc5F)C#N)CN(C2=O)C6CCC(=O)NC6=O
ACDLabs 12.01O=C1NC(=O)CCC1N1Cc2c(cccc2OCc2ccc(cc2)CN2CCN(CC2)c2ccc(C#N)cc2F)C1=O
CACTVS 3.385Fc1cc(ccc1N2CCN(CC2)Cc3ccc(COc4cccc5C(=O)N(Cc45)[CH]6CCC(=O)NC6=O)cc3)C#N
OpenEye OEToolkits 2.0.7c1cc2c(c(c1)OCc3ccc(cc3)CN4CCN(CC4)c5ccc(cc5F)C#N)CN(C2=O)[C@H]6CCC(=O)NC6=O
FormulaC32 H30 F N5 O4
NameMezigdomide
ChEMBLCHEMBL4648616
DrugBankDB17584
ZINC
PDB chain8d7u 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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PDB8d7u Molecular glue CELMoD compounds are regulators of cereblon conformation.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		F102 F150 N351 P352 H378 S379 W380 W386 F402
Binding residue
(residue number reindexed from 1)		F61 F109 N310 P311 H337 S338 W339 W345 F361
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:8d7u, PDBe:8d7u, PDBj:8d7u
PDBsum8d7u
PubMed36378961
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

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