Structure of PDB 5ynq Chain A Binding Site BS02

Receptor Information

>5ynq Chain A (length=291) Species: 1235996 (Human betacoronavirus 2c EMC/2012)

ASADWKPGHAMPSLFKVQNVNLERCELANYKQSIPMPVHMNIAKYMQLCQ
YLNTCTLAVPANMRVIHFGAGSDKGIAPGTSVLRQWLPTDAIIIDNDLNE
FVSDADITLFGDCVTVRVGQQVDLVISDMYDPTTKNVTGSNESKALFFTY
LCNLINNNLALGGSVAIKITEHSWSVELYELMGKFAWWTVFCTNANASSS
EGFLLGINYLGTIKENIDGGAMHANYIFWRNSTPMNLSTYSLFDLSKFQL
KLKGTPVLQLKESQINELVISLLSQGKLLIRDNDTLSVSTD

Ligand information

• Ligand ID: GTG
• InChI: InChI=1S/C21H29N10O18P3/c1-29-5-31(15-9(29)17(37)28-21(23)26-15)19-13(35)11(33)7(47-19)3-45-51(40,41)49-52(42,43)48-50(38,39)44-2-6-10(32)12(34)18(46-6)30-4-24-8-14(30)25-20(22)27-16(8)36/h4-7,10-13,18-19,32-35H,2-3H2,1H3,(H8-,22,23,25,26,27,28,36,37,38,39,40,41,42,43)/p+1/t6-,7-,10-,11-,12-,13-,18-,19-/m1/s1
• InChIKey: FHHZHGZBHYYWTG-INFSMZHSSA-O
• SMILES:
  CACTVS 3.385: 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(=O)NC(=Nc45)N)[C@@H](O)[C@H]2O)c6N=C(N)NC(=O)c16
  CACTVS 3.385: 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(=O)NC(=Nc45)N)[CH](O)[CH]2O)c6N=C(N)NC(=O)c16
  OpenEye OEToolkits 1.7.5: C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O
  ACDLabs 10.04: O=C1NC(=Nc2c1[n+](cn2C3OC(C(O)C3O)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O)C)N
  OpenEye OEToolkits 1.7.5: 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)n5cnc6c5N=C(NC6=O)N)O)O)O)O
• Formula: C21 H30 N10 O18 P3
• Name: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE;
  MRNA CAP ANALOG N7-METHYL GPPPG
• DrugBank: DB03958
• ZINC: ZINC000085547903
• PDB chain: 5ynq Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ynq Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex
• Resolution: 1.958 Å
• Binding residue (original residue number in PDB): C25 L27 Y30 Y132 P134 K137 K170 T172 E173 H174 S201 S202
• Binding residue (residue number reindexed from 1): C25 L27 Y30 Y130 P132 K135 K168 T170 E171 H172 S199 S200
• Annotation score: 2

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:5ynq, PDBe:5ynq, PDBj:5ynq
• PDBsum: 5ynq
• UniProt: K0BWD0