Structure of PDB 5ynf Chain A Binding Site BS01

Receptor Information

>5ynf Chain A (length=293) Species: 1235996 (Human betacoronavirus 2c EMC/2012)

ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPRGVHMNIAKYMQL
CQYLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDL
NEFVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFF
TYLCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANAS
SSEGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKF
QLKLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTD

Ligand information

• Ligand ID: GTA
• InChI: InChI=1S/C21H29N10O17P3/c1-29-6-31(17-10(29)18(36)28-21(23)27-17)20-14(35)12(33)8(46-20)3-44-50(39,40)48-51(41,42)47-49(37,38)43-2-7-11(32)13(34)19(45-7)30-5-26-9-15(22)24-4-25-16(9)30/h4-8,11-14,19-20,32-35H,2-3H2,1H3,(H7-,22,23,24,25,27,28,36,37,38,39,40,41,42)/p+1/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1
• InChIKey: QQOHNVHGNZYSBP-XPWFQUROSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: C[n+]1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O
  OpenEye OEToolkits 1.5.0: C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O
  CACTVS 3.341: C[n+]1cn([C@@H]2O[C@H](CO[P@](O)(=O)O[P@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O)c6N=C(N)NC(=O)c16
  CACTVS 3.341: C[n+]1cn([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O)c6N=C(N)NC(=O)c16
  ACDLabs 10.04: O=C1NC(=Nc2c1[n+](cn2C3OC(C(O)C3O)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)N
• Formula: C21 H30 N10 O17 P3
• Name: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE;
  7-METHYL-GPPPA
• DrugBank: DB01649
• ZINC: ZINC000096006025
• PDB chain: 5ynf Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ynf Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex
• Resolution: 1.791 Å
• Binding residue (original residue number in PDB): C25 L27 Y30 K31 Y132 K137 K170 T172 E173 H174 S201 S202
• Binding residue (residue number reindexed from 1): C25 L27 Y30 K31 Y132 K137 K170 T172 E173 H174 S201 S202
• Annotation score: 3

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

External links

• PDB: RCSB:5ynf, PDBe:5ynf, PDBj:5ynf
• PDBsum: 5ynf
• UniProt: K0BWD0