Structure of PDB 8p5a Chain B Binding Site BS01

Receptor Information
>8p5a Chain B (length=305) 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
SGVTF
Ligand information
Ligand IDX77
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-/m1/s1
InChIKeyMUNFBYOTGGMQOS-XMMPIXPASA-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@H](c2cccnc2)C(=O)NC3CCCCC3)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
ACDLabs 12.01C(=O)(N(C(c1cccnc1)C(NC2CCCCC2)=O)c3ccc(C(C)(C)C)cc3)c4cncn4
CACTVS 3.385CC(C)(C)c1ccc(cc1)N([C@@H](C(=O)NC2CCCCC2)c3cccnc3)C(=O)c4c[nH]cn4
FormulaC27 H33 N5 O2
NameN-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain8p5a Chain B Residue 406 [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]
PDB8p5a Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease.
Resolution1.66 Å
Binding residue
(original residue number in PDB)
T25 H41 F140 L141 N142 G143 S144 C145 H164 M165 E166 Q189
Binding residue
(residue number reindexed from 1)
T25 H41 F140 L141 N142 G143 S144 C145 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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:8p5a, PDBe:8p5a, PDBj:8p5a
PDBsum8p5a
PubMed38051605
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]