Structure of PDB 5yn8 Chain A Binding Site BS01

Receptor Information
>5yn8 Chain A (length=281) Species: 1235996 (Human betacoronavirus 2c EMC/2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SADWKPGHAMPSLFKVQNVNLERCELANIPMPGVHMNIAKYMQLCQYLNT
CTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNEFVSD
ADITLFGDCVTVRVGQQVDLVISDMYDPTSNESKALFFTYLCNLINNNLA
LGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSSEGFLLGINYL
GTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQLKLKGTPVLQL
KESQINELVISLLSQGKLLIRDNDTLSVSTD
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain5yn8 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

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PDB5yn8 Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex
Resolution1.97 Å
Binding residue
(original residue number in PDB)		N43 Y47 G71 A72 G73 P80 G81 D99 L100 C115 D130 M131 Y132
Binding residue
(residue number reindexed from 1)		N37 Y41 G65 A66 G67 P74 G75 D93 L94 C109 D124 M125 Y126
Annotation score5
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:5yn8, PDBe:5yn8, PDBj:5yn8
PDBsum5yn8
PubMed
UniProtK0BWD0

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