Structure of PDB 8dpr Chain A Binding Site BS01

Receptor Information
>8dpr Chain A (length=303) 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]
GSGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDM
LNPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTP
KYKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVG
FNIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTT
ITVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDI
LGPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ
CSG
Ligand information
Ligand IDT43
InChIInChI=1S/C30H35F4N5O4S2/c1-28(2,3)22(38-27(43)30(32,33)34)26(42)39-12-14-18(29(14,4)5)20(39)24(44)36-16(11-13-9-10-35-23(13)41)21(40)25-37-19-15(31)7-6-8-17(19)45-25/h6-8,13-14,16,18,20,22H,9-12H2,1-5H3,(H,35,41)(H,36,44)(H,38,43)/t13-,14-,16-,18-,20-,22+/m0/s1
InChIKeyGDKLDALGJZVEKT-MCUUEWDYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=S)N[CH](C[CH]3CCNC3=O)C(=O)c4sc5cccc(F)c5n4)C2(C)C
OpenEye OEToolkits 2.0.7CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=S)N[C@@H](C[C@@H]3CCNC3=O)C(=O)c4nc5c(cccc5s4)F)C
CACTVS 3.385CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=S)N[C@@H](C[C@@H]3CCNC3=O)C(=O)c4sc5cccc(F)c5n4)C2(C)C
ACDLabs 12.01FC(F)(F)C(=O)NC(C(=O)N1CC2C(C1C(=S)NC(CC1CCNC1=O)C(=O)c1nc3c(F)cccc3s1)C2(C)C)C(C)(C)C
OpenEye OEToolkits 2.0.7CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=S)NC(CC3CCNC3=O)C(=O)c4nc5c(cccc5s4)F)C
FormulaC30 H35 F4 N5 O4 S2
Name2,2,2-trifluoro-N-{(2S)-1-[(1R,2S,5S)-2-({(2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamothioyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}acetamide
ChEMBL
DrugBank
ZINC
PDB chain8dpr 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]
PDB8dpr Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T25 H41 M49 C145 H163 H164 M165 E166 L167 Q189 T190 Q192
Binding residue
(residue number reindexed from 1)		T26 H42 M50 C146 H164 H165 M166 E167 L168 Q190 T191 Q193
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:8dpr, PDBe:8dpr, PDBj:8dpr
PDBsum8dpr
PubMed36841831
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]