Structure of PDB 8okn Chain A Binding Site BS01

Receptor Information
>8okn 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 ID83W
InChIInChI=1S/C25H44N4O7/c1-15(35-24(2,3)4)19(28-23(34)36-25(5,6)7)22(33)29-12-8-9-18(29)21(32)27-17(14-30)13-16-10-11-26-20(16)31/h15-19,30H,8-14H2,1-7H3,(H,26,31)(H,27,32)(H,28,34)/t15-,16+,17+,18+,19+/m1/s1
InChIKeyFREYRXXGOYXVLM-BCYZHJNNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](OC(C)(C)C)[CH](NC(=O)OC(C)(C)C)C(=O)N1CCC[CH]1C(=O)N[CH](CO)C[CH]2CCNC2=O
CACTVS 3.385C[C@@H](OC(C)(C)C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CCC[C@H]1C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
OpenEye OEToolkits 2.0.7C[C@H]([C@@H](C(=O)N1CCC[C@H]1C(=O)N[C@@H](C[C@@H]2CCNC2=O)CO)NC(=O)OC(C)(C)C)OC(C)(C)C
OpenEye OEToolkits 2.0.7CC(C(C(=O)N1CCCC1C(=O)NC(CC2CCNC2=O)CO)NC(=O)OC(C)(C)C)OC(C)(C)C
FormulaC25 H44 N4 O7
Nametert-butyl-N-[(2S,3R)-3-[(2-methylpropan-2-yl)oxy]-1-oxidanylidene-1-[(2S)-2-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]pyrrolidin-1-yl]butan-2-yl]carbamate;
tert-butyl-N-[(2S,3R)-3-[(2-methylpropan-2-yl)oxy]-1-oxidanylidene-1-[(2S)-2-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]pyrrolidin-1-yl]butan-2-yl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain8okn 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]
PDB8okn Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.
Resolution1.35 Å
Binding residue
(original residue number in PDB)
F140 N142 G143 C145 H163 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
F140 N142 G143 C145 H163 H164 M165 E166 Q189
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:8okn, PDBe:8okn, PDBj:8okn
PDBsum8okn
PubMed37043904
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]