Structure of PDB 6v0n Chain A Binding Site BS02

Receptor Information
>6v0n Chain A (length=624) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRP
GPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNF
GAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDL
RDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLP
SNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQ
FIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQ
PLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMV
LGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQV
TVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVS
IPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLS
APQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDI
TLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWY
EWAVTAPVCSAIHNPTGRSYTIGL
Ligand information
Ligand IDSFG
InChIInChI=1S/C15H23N7O5/c16-6(1-2-7(17)15(25)26)3-8-10(23)11(24)14(27-8)22-5-21-9-12(18)19-4-20-13(9)22/h4-8,10-11,14,23-24H,1-3,16-17H2,(H,25,26)(H2,18,19,20)/t6-,7-,8+,10+,11+,14+/m0/s1
InChIKeyLMXOHSDXUQEUSF-YECHIGJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CC(CCC(C(=O)O)N)N)O)O)N
CACTVS 3.370N[CH](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
CACTVS 3.370N[C@@H](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(O)C(N)CCC(N)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC15 H23 N7 O5
NameSINEFUNGIN;
ADENOSYL-ORNITHINE
ChEMBLCHEMBL1214186
DrugBankDB01910
ZINCZINC000004217451
PDB chain6v0n Chain A Residue 701 [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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PDB6v0n Molecular basis for substrate recruitment to the PRMT5 methylosome.
Resolution2.11 Å
Binding residue
(original residue number in PDB)		P314 L315 Y324 Y334 G365 P370 E392 K393 D419 M420 E435 L436 C449
Binding residue
(residue number reindexed from 1)		P301 L302 Y311 Y321 G352 P357 E379 K380 D406 M407 E422 L423 C436
Annotation score3
Binding affinityBindingDB: IC50=8600nM
Enzymatic activity
Enzyme Commision number 2.1.1.320: type II protein arginine methyltransferase.
Gene Ontology
Molecular Function
GO:0002039 p53 binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
GO:0008327 methyl-CpG binding
GO:0008469 histone arginine N-methyltransferase activity
GO:0016274 protein-arginine N-methyltransferase activity
GO:0035243 protein-arginine omega-N symmetric methyltransferase activity
GO:0042054 histone methyltransferase activity
GO:0042802 identical protein binding
GO:0043021 ribonucleoprotein complex binding
GO:0044020 histone H4R3 methyltransferase activity
GO:0044877 protein-containing complex binding
GO:0046982 protein heterodimerization activity
GO:0070888 E-box binding
GO:0140938 histone H3 methyltransferase activity
Biological Process
GO:0000387 spliceosomal snRNP assembly
GO:0006325 chromatin organization
GO:0006338 chromatin remodeling
GO:0006353 DNA-templated transcription termination
GO:0006355 regulation of DNA-templated transcription
GO:0006479 protein methylation
GO:0007088 regulation of mitotic nuclear division
GO:0010468 regulation of gene expression
GO:0018216 peptidyl-arginine methylation
GO:0032259 methylation
GO:0032922 circadian regulation of gene expression
GO:0035246 peptidyl-arginine N-methylation
GO:0042118 endothelial cell activation
GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation
GO:0045596 negative regulation of cell differentiation
GO:0045892 negative regulation of DNA-templated transcription
GO:0048026 positive regulation of mRNA splicing, via spliceosome
GO:0048511 rhythmic process
GO:0048714 positive regulation of oligodendrocyte differentiation
GO:0070372 regulation of ERK1 and ERK2 cascade
GO:0090161 Golgi ribbon formation
GO:0097421 liver regeneration
GO:1901796 regulation of signal transduction by p53 class mediator
GO:1904992 positive regulation of adenylate cyclase-inhibiting dopamine receptor signaling pathway
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0034709 methylosome
GO:0035097 histone methyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6v0n, PDBe:6v0n, PDBj:6v0n
PDBsum6v0n
PubMed34358446
UniProtO14744|ANM5_HUMAN Protein arginine N-methyltransferase 5 (Gene Name=PRMT5)

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