Structure of PDB 8p5c Chain A Binding Site BS01

Receptor Information
>8p5c 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 ID9M5
InChIInChI=1S/C27H33N5O2/c1-27(2,3)20-11-13-22(14-12-20)32(26(34)23-17-29-18-30-23)24(19-8-7-15-28-16-19)25(33)31-21-9-5-4-6-10-21/h7-8,11-18,21,24H,4-6,9-10H2,1-3H3,(H,29,30)(H,31,33)/t24-/m0/s1
InChIKeyMUNFBYOTGGMQOS-DEOSSOPVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([CH](C(=O)NC2CCCCC2)c3cccnc3)C(=O)c4c[nH]cn4
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccc(cc1)N(C(c2cccnc2)C(=O)NC3CCCCC3)C(=O)c4c[nH]cn4
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([C@H](C(=O)NC2CCCCC2)c3cccnc3)C(=O)c4c[nH]cn4
OpenEye OEToolkits 2.0.7CC(C)(C)c1ccc(cc1)N([C@@H](c2cccnc2)C(=O)NC3CCCCC3)C(=O)c4c[nH]cn4
FormulaC27 H33 N5 O2
Name~{N}-(4-~{tert}-butylphenyl)-~{N}-[(1~{S})-2-(cyclohexylamino)-2-oxidanylidene-1-pyridin-3-yl-ethyl]-1~{H}-imidazole-4-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8p5c Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8p5c Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.
Resolution1.51 Å
Binding residue
(original residue number in PDB)
H41 M49 F140 L141 N142 C145 H163 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
H41 M49 F140 L141 N142 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

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Molecular Function

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Biological Process
External links
PDB RCSB:8p5c, PDBe:8p5c, PDBj:8p5c
PDBsum8p5c
PubMed38051605
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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