Structure of PDB 8f4y Chain A Binding Site BS01

Receptor Information
>8f4y Chain A (length=298) 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]
SSQAWQPGVAMPNLYKMQRMLLEKCDLQNYGDSATLPKGIMMNVAKYTQL
CQYLNTLTLAVPYNMRVIHFGAGSDKGVAPGTAVLRQWLPTGTLLVDSDL
NDFVSDADSTLIGDCATVHTANKWDLIISDMYDPKTKNVTKENDSKEGFF
TYICGFIQQKLALGGSVAIKITEHSWNADLYKLMGHFAWWTAFVTNVNAS
SSEAFLIGCNYLGKPREQIDGYVMHANYIFWRNTNPIQLSSYSLFDMSKF
PLKLRGTAVMSLKEGQINDMILSLLSKGRLIIRENNRVVISSDVLVNN
Ligand information
Ligand IDXDU
InChIInChI=1S/C13H7Cl2F3N2O/c14-8-3-1-7(10(15)5-8)2-4-9-6-11(13(16,17)18)20-12(21)19-9/h1-6H,(H,19,20,21)/b4-2+
InChIKeyMMOUYBCDJMEUFG-DUXPYHPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(c(cc1Cl)Cl)C=Cc2cc(nc(n2)O)C(F)(F)F
CACTVS 3.385Oc1nc(\C=C\c2ccc(Cl)cc2Cl)cc(n1)C(F)(F)F
ACDLabs 12.01Oc1nc(/C=C/c2ccc(Cl)cc2Cl)cc(n1)C(F)(F)F
CACTVS 3.385Oc1nc(C=Cc2ccc(Cl)cc2Cl)cc(n1)C(F)(F)F
OpenEye OEToolkits 2.0.7c1cc(c(cc1Cl)Cl)/C=C/c2cc(nc(n2)O)C(F)(F)F
FormulaC13 H7 Cl2 F3 N2 O
Name4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol
ChEMBLCHEMBL1308276
DrugBank
ZINCZINC000004954956
PDB chain8f4y Chain A Residue 7102 [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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PDB8f4y Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors.
Resolution2.13 Å
Binding residue
(original residue number in PDB)		F6868 C6913 V6916 H6917 T6918 M6929 F6947 I6951 F6954 I7088
Binding residue
(residue number reindexed from 1)		F70 C115 V118 H119 T120 M131 F149 I153 F156 I290
Annotation score1
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:8f4y, PDBe:8f4y, PDBj:8f4y
PDBsum8f4y
PubMed37728236
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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