Structure of PDB 4onm Chain B Binding Site BS01

Receptor Information
>4onm Chain B (length=149) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGLPRRIIKETQRLLAEPVPGIKAEPDESNARYFHVVIAGPQDSPFEGGT
FKLELFLPEEYPMAAPKVRFMTKIYHPNVDKLGRICLDILKDKWSPALQI
RTVLLSIQALLSAPNPDDPLANDVAEQWKTNEAQAIETARAWTRLYAMN
Ligand information
Ligand IDN2F
InChIInChI=1S/C11H9NO5S/c1-8-2-4-9(5-3-8)18(15,16)11-7-6-10(17-11)12(13)14/h2-7H,1H3
InChIKeyGAUHIPWCDXOLCZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6Cc1ccc(cc1)S(=O)(=O)c2ccc(o2)[N+](=O)[O-]
ACDLabs 12.01O=[N+]([O-])c1oc(cc1)S(=O)(=O)c2ccc(cc2)C
CACTVS 3.385Cc1ccc(cc1)[S](=O)(=O)c2oc(cc2)[N+]([O-])=O
FormulaC11 H9 N O5 S
Name2-[(4-methylphenyl)sulfonyl]-5-nitrofuran;
NSC697923
ChEMBLCHEMBL1698008
DrugBank
ZINCZINC000001860216
PDB chain4onm Chain B Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4onm Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting.
Resolution1.35 Å
Binding residue
(original residue number in PDB)		N79 V80 D81 R85 I86 C87 L121 N123
Binding residue
(residue number reindexed from 1)		N78 V79 D80 R84 I85 C86 L120 N122
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C87
Catalytic site (residue number reindexed from 1) C86
Enzyme Commision number 2.3.2.23: E2 ubiquitin-conjugating enzyme.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0019787 ubiquitin-like protein transferase activity
GO:0031625 ubiquitin protein ligase binding
GO:0043130 ubiquitin binding
GO:0061631 ubiquitin conjugating enzyme activity
GO:0097027 ubiquitin-protein transferase activator activity
Biological Process
GO:0000209 protein polyubiquitination
GO:0000724 double-strand break repair via homologous recombination
GO:0000729 DNA double-strand break processing
GO:0006281 DNA repair
GO:0006282 regulation of DNA repair
GO:0006301 postreplication repair
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006513 protein monoubiquitination
GO:0016567 protein ubiquitination
GO:0043123 positive regulation of canonical NF-kappaB signal transduction
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045739 positive regulation of DNA repair
GO:0050852 T cell receptor signaling pathway
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0070534 protein K63-linked ubiquitination
GO:0140374 antiviral innate immune response
GO:1902523 positive regulation of protein K63-linked ubiquitination
GO:1902533 positive regulation of intracellular signal transduction
GO:1904262 negative regulation of TORC1 signaling
GO:2000781 positive regulation of double-strand break repair
Cellular Component
GO:0000151 ubiquitin ligase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0031371 ubiquitin conjugating enzyme complex
GO:0031372 UBC13-MMS2 complex
GO:0032991 protein-containing complex
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4onm, PDBe:4onm, PDBj:4onm
PDBsum4onm
PubMed25909880
UniProtP61088|UBE2N_HUMAN Ubiquitin-conjugating enzyme E2 N (Gene Name=UBE2N)

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