Structure of PDB 4ci3 Chain B Binding Site BS02

Receptor Information
>4ci3 Chain B (length=370) Species: 9031 (Gallus gallus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MINFDTSLPTSHMYLGSDMEEFHGRTLHDDDSCQVIPVLPHVMVMLIPGQ
TLPLQLFHPQEVSMVRNLIQKDRTFAVLAYSNVREREAHFGTTAEIYAYR
EEQEYGIETVKVKAIGRQRFKVLEIRTQSDGIQQAKVQILPERVLPSTMS
AVQLQSLSRRHIRAFRQWWQKYQKRKFHCASLTSWPPWLYSLYDAETLME
RVKRQLHEWDENLKDESLPTNPIDFSYRVAACLPIDDALRIQLLKIGSAI
QRLRCELDIMNKCTSLCCKQCQDTEITTKNEIFSLSLCGPMAAYVNPHGY
IHETLTVYKACNLNLSGRPSTEHSWFPGYAWTIAQCRICGNHMGWKFTAT
KKDMSPQKFWGLTRSALLPR
Ligand information
Ligand IDY70
InChIInChI=1S/C13H11N3O4/c14-7-3-1-2-6-10(7)13(20)16(12(6)19)8-4-5-9(17)15-11(8)18/h1-3,8H,4-5,14H2,(H,15,17,18)/t8-/m0/s1
InChIKeyUVSMNLNDYGZFPF-QMMMGPOBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1NC(=O)CCC1N3C(=O)c2cccc(c2C3=O)N
CACTVS 3.385Nc1cccc2C(=O)N([C@H]3CCC(=O)NC3=O)C(=O)c12
OpenEye OEToolkits 1.9.2c1cc2c(c(c1)N)C(=O)N(C2=O)[C@H]3CCC(=O)NC3=O
CACTVS 3.385Nc1cccc2C(=O)N([CH]3CCC(=O)NC3=O)C(=O)c12
OpenEye OEToolkits 1.9.2c1cc2c(c(c1)N)C(=O)N(C2=O)C3CCC(=O)NC3=O
FormulaC13 H11 N3 O4
NameS-Pomalidomide
ChEMBLCHEMBL2093113
DrugBank
ZINCZINC000003940470
PDB chain4ci3 Chain B Residue 1429 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ci3 Structure of the Ddb1-Crbn E3 Ubiquitin Ligase in Complex with Thalidomide.
Resolution3.5 Å
Binding residue
(original residue number in PDB)		N353 P354 H355 H380 S381 W382 W388 W402 F404
Binding residue
(residue number reindexed from 1)		N296 P297 H298 H323 S324 W325 W331 W345 F347
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.81,Kd=156.6nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0046872 metal ion binding
Biological Process
GO:0016567 protein ubiquitination
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0031464 Cul4A-RING E3 ubiquitin ligase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4ci3, PDBe:4ci3, PDBj:4ci3
PDBsum4ci3
PubMed25043012
UniProtP0CF65|CRBN_CHICK Protein cereblon (Gene Name=CRBN)

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