Structure of PDB 7dfg Chain A Binding Site BS03

Receptor Information
>7dfg Chain A (length=908) 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]
QSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCC
RFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFKF
RIDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDY
FNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLT
LDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAESH
VDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRC
ILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHN
QDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNVA
FQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYY
RYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFPF
NKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRART
VAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVY
SDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLA
NECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNA
LLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMM
ILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDLT
KGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMI
ERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTTSRYWEPEFY
EAMYTPHT
Ligand information
Ligand ID1RP
InChIInChI=1S/C10H13FN3O9P/c11-4-1-14(9(18)5(13-4)8(12)17)10-7(16)6(15)3(23-10)2-22-24(19,20)21/h1,3,6-7,10,15-16H,2H2,(H2,12,17)(H2,19,20,21)/t3-,6-,7-,10-/m1/s1
InChIKeyRWCWUNIDADUVEZ-KAFVXXCXSA-N
SMILES
SoftwareSMILES
CACTVS 3.370NC(=O)C1=NC(=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)F
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)C(=NC(F)=C1)C(=O)N)C(O)C2O
OpenEye OEToolkits 1.7.6C1=C(N=C(C(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)C(=O)N)F
OpenEye OEToolkits 1.7.6C1=C(N=C(C(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)N)F
CACTVS 3.370NC(=O)C1=NC(=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)F
FormulaC10 H13 F N3 O9 P
Name6-fluoro-3-oxo-4-(5-O-phosphono-beta-D-ribofuranosyl)-3,4-dihydropyrazine-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000098208017
PDB chain7dfg Chain P Residue 1201 [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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PDB7dfg Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
Resolution2.7 Å
Binding residue
(original residue number in PDB)		D623 S682 D760
Binding residue
(residue number reindexed from 1)		D617 S676 D754
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:7dfg, PDBe:7dfg, PDBj:7dfg
PDBsum7dfg
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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