Structure of PDB 7ed5 Chain A Binding Site BS06

Receptor Information
>7ed5 Chain A (length=926) 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]
AQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNC
CRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFK
FRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCD
DDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVG
VLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTA
ESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLD
DRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGV
VHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTN
NVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDY
DYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAG
FPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNR
ARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLK
TVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFY
RLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTAN
VNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHF
SMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTET
DLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGT
LMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMY
SVMLTNDNTSRYWEPEFYEAMYTPHT
Ligand information
Ligand IDAT9
InChIInChI=1S/C11H17FN5O13P3/c1-11(12)6(18)4(2-27-32(23,24)30-33(25,26)29-31(20,21)22)28-9(11)17-3-14-5-7(17)15-10(13)16-8(5)19/h3-4,6,9,18H,2H2,1H3,(H,23,24)(H,25,26)(H2,20,21,22)(H3,13,15,16,19)/t4-,6-,9-,11-/m1/s1
InChIKeyGFEXCNGIPRYQFE-GITKWUPZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@]1(F)[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]1n2cnc3C(=O)NC(=Nc23)N
OpenEye OEToolkits 2.0.7CC1(C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F
CACTVS 3.385C[C]1(F)[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]1n2cnc3C(=O)NC(=Nc23)N
OpenEye OEToolkits 2.0.7C[C@]1([C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F
FormulaC11 H17 F N5 O13 P3
Name[[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate;
AT-9010
ChEMBLCHEMBL1630001
DrugBank
ZINCZINC000066258646
PDB chain7ed5 Chain A Residue 1004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7ed5 A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase.
Resolution2.98 Å
Binding residue
(original residue number in PDB)		F35 K50 C53 R55 V71 K73 R116 L119 T120 K121 Y217 D218
Binding residue
(residue number reindexed from 1)		F32 K47 C50 R52 V68 K70 R113 L116 T117 K118 Y214 D215
Annotation score2
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:0003723 RNA binding
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005524 ATP binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0039694 viral RNA genome replication

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7ed5, PDBe:7ed5, PDBj:7ed5
PDBsum7ed5
PubMed35110538
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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