Structure of PDB 7krn Chain A Binding Site BS08

Receptor Information
>7krn Chain A (length=927) 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]
DAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTN
CCRFQEKDEDDNLIDSYFVVKRHTFSNYQHEETIYNLLKDCPAVAKHDFF
KFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCC
DDDYFNKKDWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIV
GVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSLLMPILTLTRALT
AESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCL
DDRCILHCANFNVLFSTVFPPTSFGPLVRKIFVDGVPFVVSTGYHFRELG
VVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAALT
NNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISD
YDYYRYNLPTMCDIRQLLFVVEVVDKYFDCYDGGCINANQVIVNNLDKSA
GFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKN
RARTVAGVSICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNML
KTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRF
YRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTA
NVNALLSTDGNKIADKYVRNLQHRLYECLYRNRDVDTDFVNEFYAYLRKH
FSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCWTE
TDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDG
TLMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDM
YSVMLTNDNTSRYWEPEFYEAMYTPHT
Ligand information
Ligand ID1N7
InChIInChI=1S/C32H58N2O8S/c1-20(7-10-29(39)33-13-6-14-34(4,5)18-23(36)19-43(40,41)42)24-8-9-25-30-26(17-28(38)32(24,25)3)31(2)12-11-22(35)15-21(31)16-27(30)37/h20-28,30,35-38H,6-19H2,1-5H3,(H-,33,39,40,41,42)/p+1/t20-,21+,22-,23?,24-,25+,26+,27-,28+,30+,31+,32-/m1/s1
InChIKeyGUQQBLRVXOUDTN-XOHPMCGNSA-O
SMILES
SoftwareSMILES
CACTVS 3.370C[C@H](CCC(=O)NCCC[N+](C)(C)CC(O)C[S](O)(=O)=O)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C
ACDLabs 12.01O=S(=O)(O)CC(O)C[N+](C)(C)CCCNC(=O)CCC(C3CCC2C1C(O)CC4CC(O)CCC4(C)C1CC(O)C23C)C
OpenEye OEToolkits 1.7.6C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C@H]3[C@H]2[C@@H](C[C@H]4[C@@]3(CC[C@H](C4)O)C)O)O)C
OpenEye OEToolkits 1.7.6CC(CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)C1CCC2C1(C(CC3C2C(CC4C3(CCC(C4)O)C)O)O)C
CACTVS 3.370C[CH](CCC(=O)NCCC[N+](C)(C)CC(O)C[S](O)(=O)=O)[CH]1CC[CH]2[CH]3[CH](O)C[CH]4C[CH](O)CC[C]4(C)[CH]3C[CH](O)[C]12C
FormulaC32 H59 N2 O8 S
NameCHAPSO;
2-hydroxy-N,N-dimethyl-3-sulfo-N-(3-{[(3beta,5beta,7beta,12beta)-3,7,12-trihydroxy-24-oxocholan-24-yl]amino}propyl)propan-1-aminium
ChEMBL
DrugBank
ZINC
PDB chain7krn Chain A Residue 1006 [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]
PDB7krn Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex.
Resolution3.4 Å
Binding residue
(original residue number in PDB)
R197 V231 Y289
Binding residue
(residue number reindexed from 1)
R195 V229 Y287
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: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:7krn, PDBe:7krn, PDBj:7krn
PDBsum7krn
PubMed33883267
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]