Structure of PDB 8okk Chain B Binding Site BS01

Receptor Information
>8okk Chain B (length=306) 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
SGVTFQ
Ligand information
Ligand ID83F
InChIInChI=1S/C23H40N4O6/c1-13(2)18(26-22(32)33-23(4,5)6)21(31)27-11-14(3)9-17(27)20(30)25-16(12-28)10-15-7-8-24-19(15)29/h13-18,28H,7-12H2,1-6H3,(H,24,29)(H,25,30)(H,26,32)/t14-,15-,16-,17-,18-/m0/s1
InChIKeyCUINDADQQONHSA-ATIWLJMLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC1CC(N(C1)C(=O)C(C(C)C)NC(=O)OC(C)(C)C)C(=O)NC(CC2CCNC2=O)CO
CACTVS 3.385CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1C[C@@H](C)C[C@H]1C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
CACTVS 3.385CC(C)[CH](NC(=O)OC(C)(C)C)C(=O)N1C[CH](C)C[CH]1C(=O)N[CH](CO)C[CH]2CCNC2=O
OpenEye OEToolkits 2.0.7C[C@H]1C[C@H](N(C1)C(=O)[C@H](C(C)C)NC(=O)OC(C)(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)CO
FormulaC23 H40 N4 O6
Nametert-butyl-N-[(2S)-3-methyl-1-[(2S,4S)-4-methyl-2-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]carbamate;
tert-butyl N-[(2S)-3-methyl-1-[(2S,4S)-4-methyl-2-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain8okk Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8okk 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.
Resolution1.63 Å
Binding residue
(original residue number in PDB)
M49 F140 N142 G143 C145 H163 H164 M165 E166 Q189 Q192
Binding residue
(residue number reindexed from 1)
M49 F140 N142 G143 C145 H163 H164 M165 E166 Q189 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

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Molecular Function

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Biological Process
External links
PDB RCSB:8okk, PDBe:8okk, PDBj:8okk
PDBsum8okk
PubMed37043904
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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