Structure of PDB 7dfh Chain A Binding Site BS05

Receptor Information
>7dfh 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
ERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELNTSRYWEPEFY
EAMYTPHT
Ligand information
Ligand IDRVP
InChIInChI=1S/C8H13N4O8P/c9-6(15)7-10-2-12(11-7)8-5(14)4(13)3(20-8)1-19-21(16,17)18/h2-5,8,13-14H,1H2,(H2,9,15)(H2,16,17,18)/t3-,4-,5-,8-/m1/s1
InChIKeySDWIOXKHTFOULX-AFCXAGJDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(nn1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ncn(n1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=C(c1ncn(n1)C2OC(C(O)C2O)COP(=O)(O)O)N
CACTVS 3.341NC(=O)c1ncn(n1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(nn1C2C(C(C(O2)COP(=O)(O)O)O)O)C(=O)N
FormulaC8 H13 N4 O8 P
NameRIBAVIRIN MONOPHOSPHATE
ChEMBLCHEMBL1235764
DrugBankDB14663
ZINCZINC000012402859
PDB chain7dfh 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7dfh Structural basis for repurpose and design of nucleotide drugs for treating COVID-19
Resolution2.97 Å
Binding residue
(original residue number in PDB)		R555 D623 S682 N691 D760
Binding residue
(residue number reindexed from 1)		R549 D617 S676 N685 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:7dfh, PDBe:7dfh, PDBj:7dfh
PDBsum7dfh
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]