Structure of PDB 5ynn Chain A Binding Site BS01

Receptor Information
>5ynn Chain A (length=295) Species: 1235996 (Human betacoronavirus 2c EMC/2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPRGVHMNIAKYMQL
CQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDL
NEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFF
TYLCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANAS
SSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKF
QLKLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTDVL
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 chain5ynn Chain A Residue 401 [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]
PDB5ynn Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex
Resolution1.86 Å
Binding residue
(original residue number in PDB)		N43 G71 G73 D99 L100 D114 C115 D130 M131
Binding residue
(residue number reindexed from 1)		N43 G71 G73 D99 L100 D114 C115 D130 M131
Annotation score3
Enzymatic activity
Enzyme Commision number 2.1.1.57: methyltransferase cap1.
3.4.19.12: ubiquitinyl hydrolase 1.
3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
Gene Ontology
Molecular Function
GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:5ynn, PDBe:5ynn, PDBj:5ynn
PDBsum5ynn
PubMed
UniProtK0BWD0

[Back to BioLiP]