Structure of PDB 9eml Chain A Binding Site BS01

Receptor Information
>9eml Chain A (length=300) 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]
SQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQLC
QYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDLN
DFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFFT
YICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNASS
SEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKFP
LKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNNENL
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 chain9eml Chain A Residue 7201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB9eml SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug development
Resolution2.4 Å
Binding residue
(original residue number in PDB)		C6823 L6825 Y6828 K6844 Y6930 K6935 K6968 T6970 E6971 H6972 S6999 S7000
Binding residue
(residue number reindexed from 1)		C24 L26 Y29 K45 Y131 K136 K169 T171 E172 H173 S200 S201
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:9eml, PDBe:9eml, PDBj:9eml
PDBsum9eml
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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