Structure of PDB 6h0f Chain B Binding Site BS02

Receptor Information
>6h0f Chain B (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 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 chain6h0f 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6h0f Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.
Resolution3.25 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
Binding affinityBindingDB: IC50=2000nM
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:6h0f, PDBe:6h0f, PDBj:6h0f
PDBsum6h0f
PubMed30385546
UniProtQ96SW2|CRBN_HUMAN Protein cereblon (Gene Name=CRBN)

[Back to BioLiP]