Structure of PDB 7lyh Chain A Binding Site BS01

Receptor Information
>7lyh Chain A (length=304) 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
SGVT
Ligand information
Ligand IDYHJ
InChIInChI=1S/C23H31N3O5/c27-13-18(11-16-9-10-24-21(16)28)25-22(29)20-19-8-4-7-17(19)12-26(20)23(30)31-14-15-5-2-1-3-6-15/h1-3,5-6,16-20,27H,4,7-14H2,(H,24,28)(H,25,29)/t16-,17-,18-,19-,20-/m0/s1
InChIKeyBQHAUUUZCGWWEE-HVTWWXFQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)COC(=O)N2CC3CCCC3C2C(=O)NC(CC4CCNC4=O)CO
CACTVS 3.385OC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H]2[C@H]3CCC[C@H]3CN2C(=O)OCc4ccccc4
CACTVS 3.385OC[CH](C[CH]1CCNC1=O)NC(=O)[CH]2[CH]3CCC[CH]3CN2C(=O)OCc4ccccc4
ACDLabs 12.01O=C1NCCC1CC(CO)NC(=O)C1C2CCCC2CN1C(=O)OCc1ccccc1
OpenEye OEToolkits 2.0.7c1ccc(cc1)COC(=O)N2C[C@@H]3CCCC3[C@H]2C(=O)N[C@@H](C[C@@H]4CCNC4=O)CO
FormulaC23 H31 N3 O5
Namebenzyl (1S,3aR,6aS)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)hexahydrocyclopenta[c]pyrrole-2(1H)-carboxylate
ChEMBL
DrugBank
ZINC
PDB chain7lyh 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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PDB7lyh Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal Structures with the Peptidomimetic Inhibitors GC-376, Telaprevir, and Boceprevir.
Resolution1.9 Å
Binding residue
(original residue number in PDB)
H41 F140 C145 H163 H164 M165 E166 D187 R188 T190
Binding residue
(residue number reindexed from 1)
H41 F140 C145 H163 H164 M165 E166 D187 R188 T190
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:7lyh, PDBe:7lyh, PDBj:7lyh
PDBsum7lyh
PubMed34414360
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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