Structure of PDB 8okb Chain A Binding Site BS01

Receptor Information
>8okb Chain A (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 IDVQR
InChIInChI=1S/C24H35N3O6/c1-16(2)13-20(27-24(31)33-15-17-7-5-4-6-8-17)23(30)26-19(9-10-21(28)32-3)14-18-11-12-25-22(18)29/h4-8,16,18-20H,9-15H2,1-3H3,(H,25,29)(H,26,30)(H,27,31)/t18-,19-,20-/m0/s1
InChIKeyJGJNNQJIGUGNAT-UFYCRDLUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CCC(=O)OC)CC1CCNC1=O)NC(=O)OCc2ccccc2
CACTVS 3.385COC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](CC(C)C)NC(=O)OCc2ccccc2
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](CCC(=O)OC)C[C@@H]1CCNC1=O)NC(=O)OCc2ccccc2
CACTVS 3.385COC(=O)CC[C@@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC(C)C)NC(=O)OCc2ccccc2
FormulaC24 H35 N3 O6
Namemethyl (4~{S})-4-[[(2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-5-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]pentanoate
ChEMBL
DrugBank
ZINC
PDB chain8okb 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

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PDB8okb Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3‐Chymotrypsin-like Protease of SARS-CoV‐2
Resolution2.31 Å
Binding residue
(original residue number in PDB)
T26 L27 H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166
Binding residue
(residue number reindexed from 1)
T26 L27 H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166
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

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Biological Process
External links
PDB RCSB:8okb, PDBe:8okb, PDBj:8okb
PDBsum8okb
PubMed38352832
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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