Structure of PDB 7jib Chain A Binding Site BS03

Receptor Information
>7jib Chain A (length=299) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQ
LCQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSD
LNDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGF
FTYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNA
SSSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSK
FPLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
Ligand information
Ligand IDGTA
InChIInChI=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
InChIKeyQQOHNVHGNZYSBP-XPWFQUROSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[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 1.5.0C[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 3.341C[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 3.341C[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 10.04O=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
FormulaC21 H30 N10 O17 P3
NameP1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE;
7-METHYL-GPPPA
ChEMBL
DrugBankDB01649
ZINCZINC000096006025
PDB chain7jib Chain A Residue 7105 [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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PDB7jib 2'-O methylation of RNA cap in SARS-CoV-2 captured by serial crystallography.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		C25 D26 L27 Y30 K46 Y132 K137 K170 T172 E173 H174 S201 S202
Binding residue
(residue number reindexed from 1)		C26 D27 L28 Y31 K47 Y133 K138 K171 T173 E174 H175 S202 S203
Annotation score3
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

View graph for
Molecular Function
External links
PDB RCSB:7jib, PDBe:7jib, PDBj:7jib
PDBsum7jib
PubMed33972410
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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