Structure of PDB 9emv Chain A Binding Site BS04

Receptor Information

>9emv Chain A (length=300) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLC
QYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLN
DFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFT
YICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASS
SEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFP
LKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNNENL

Ligand information

• Ligand ID: V9G
• InChI: InChI=1S/C22H32N10O17P3/c1-30-7-32(18-11(30)19(36)29-22(24)28-18)20-14(35)12(33)8(46-20)3-44-50(37,38)48-52(41,42)49-51(39,40)45-4-9-13(34)15(43-2)21(47-9)31-6-27-10-16(23)25-5-26-17(10)31/h5-9,12-15,20-21,33-35H,3-4H2,1-2H3,(H,37,38)(H,39,40)(H,41,42)(H2,23,25,26)(H3,24,28,29,36)/t8-,9-,12-,13-,14-,15-,20-,21-/m1/s1
• InChIKey: WZAAWBDISKLAIE-NAGRZYTCSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CN1C=[N](C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)OC)O)O)O
  OpenEye OEToolkits 2.0.7: CN1C=[N](C2=C1C(=O)NC(=N2)N)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)OC)O)O)O
  CACTVS 3.385: CO[CH]1[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)[n]3cn(C)c4C(=O)NC(=Nc34)N)O[CH]1n5cnc6c(N)ncnc56
  CACTVS 3.385: CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)[n]3cn(C)c4C(=O)NC(=Nc34)N)O[C@H]1n5cnc6c(N)ncnc56
• Formula: C22 H32 N10 O17 P3
• Name: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE
• PDB chain: 9emv Chain A Residue 7211

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9emv SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug development
• Resolution: 2.34 Å
• Binding residue (original residue number in PDB): C6823 D6824 L6825 Y6828 K6844 Y6930 P6932 K6935 K6968 T6970 E6971 H6972 S6999 S7000
• Binding residue (residue number reindexed from 1): C24 D25 L26 Y29 K45 Y131 P133 K136 K169 T171 E172 H173 S200 S201
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
  2.1.1.57: methyltransferase cap1.
  2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.50: mRNA guanylyltransferase.
  3.1.13.-
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.
  3.6.4.12: DNA helicase.
  3.6.4.13: RNA helicase.
  4.6.1.-

Gene Ontology

Molecular Function

• GO:0004483 mRNA (nucleoside-2'-O-)-methyltransferase activity

External links

• PDB: RCSB:9emv, PDBe:9emv, PDBj:9emv
• PDBsum: 9emv
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)