Structure of PDB 7doi Chain A Binding Site BS05

Receptor Information

>7doi Chain A (length=906) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

AQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNC
CRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFFK
FRIDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDD
YFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVL
TLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALTAES
HVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDR
CILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVH
NQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALTNNV
AFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDY
YRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSAGFP
FNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRAR
TVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTV
YSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRL
ANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVN
ALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSM
MILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTETDL
TKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLM
IERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELRYWEPEFYEA
MYTPHT

Ligand information

• Ligand ID: POP
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-2
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-L
• SMILES:
  OpenEye OEToolkits 1.5.0: O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
  CACTVS 3.341: O[P]([O-])(=O)O[P](O)([O-])=O
  ACDLabs 10.04: [O-]P(=O)(O)OP([O-])(=O)O
  OpenEye OEToolkits 1.5.0: OP(=O)([O-])OP(=O)(O)[O-]
• Formula: H2 O7 P2
• Name: PYROPHOSPHATE 2-
• PDB chain: 7doi Chain A Residue 1003

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7doi Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): R553 P620 K621
• Binding residue (residue number reindexed from 1): R548 P615 K616
• Annotation score: 5

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

External links

• PDB: RCSB:7doi, PDBe:7doi, PDBj:7doi
• PDBsum: 7doi
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)