Structure of PDB 8ign Chain A Binding Site BS01

Receptor Information
>8ign Chain A (length=301) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
S
Ligand information
Ligand ID7ON
InChIInChI=1S/C31H44F3N5O6/c32-31(33,34)30(45)38-23(17-7-2-1-3-8-17)29(44)39-16-19-9-6-12-21(19)24(39)27(42)37-22(15-18-13-14-35-26(18)41)25(40)28(43)36-20-10-4-5-11-20/h17-24H,1-16H2,(H,35,41)(H,36,43)(H,37,42)(H,38,45)/t18-,19-,21-,22-,23-,24-/m0/s1
InChIKeyICGMMLTUQDVAST-HEZDJTGRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385FC(F)(F)C(=O)N[CH](C1CCCCC1)C(=O)N2C[CH]3CCC[CH]3[CH]2C(=O)N[CH](C[CH]4CCNC4=O)C(=O)C(=O)NC5CCCC5
OpenEye OEToolkits 2.0.7C1CCC(CC1)C(C(=O)N2CC3CCCC3C2C(=O)NC(CC4CCNC4=O)C(=O)C(=O)NC5CCCC5)NC(=O)C(F)(F)F
OpenEye OEToolkits 2.0.7C1CCC(CC1)[C@@H](C(=O)N2C[C@@H]3CCC[C@@H]3[C@H]2C(=O)N[C@@H](C[C@@H]4CCNC4=O)C(=O)C(=O)NC5CCCC5)NC(=O)C(F)(F)F
CACTVS 3.385FC(F)(F)C(=O)N[C@@H](C1CCCCC1)C(=O)N2C[C@@H]3CCC[C@@H]3[C@H]2C(=O)N[C@@H](C[C@@H]4CCNC4=O)C(=O)C(=O)NC5CCCC5
FormulaC31 H44 F3 N5 O6
Name(3~{S},3~{a}~{S},6~{a}~{R})-2-[(2~{S})-2-cyclohexyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]ethanoyl]-~{N}-[(2~{S})-4-(cyclopentylamino)-3,4-bis(oxidanylidene)-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8ign Chain A Residue 401 [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]
PDB8ign Inhibition mechanism and antiviral activity of an alpha-ketoamide based SARS-CoV-2 main protease inhibitor
Resolution2.02 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 D187 R188 T190 Q192
Binding residue
(residue number reindexed from 1)
H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 D187 R188 T190 Q192
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:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:8ign, PDBe:8ign, PDBj:8ign
PDBsum8ign
PubMed38553607
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]