Structure of PDB 8j39 Chain B Binding Site BS01

Receptor Information
>8j39 Chain B (length=299) 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]
GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFFDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Ligand information
Ligand IDV2M
InChIInChI=1S/C24H34N4O6/c1-13(2)9-18(23(32)27-17(20(30)12-29)10-14-7-8-25-22(14)31)28-24(33)19-11-15-16(26-19)5-4-6-21(15)34-3/h4-6,11,13-14,17-18,20,26,29-30H,7-10,12H2,1-3H3,(H,25,31)(H,27,32)(H,28,33)/t14-,17-,18-,20+/m0/s1
InChIKeyFDQSUXUTXIGUIA-PRIDNEQBSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01COc1cccc2[NH]c(cc12)C(=O)NC(CC(C)C)C(=O)NC(CC1CCNC1=O)C(O)CO
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CC1CCNC1=O)C(CO)O)NC(=O)c2cc3c([nH]2)cccc3OC
CACTVS 3.385COc1cccc2[nH]c(cc12)C(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)CO
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](CO)O)NC(=O)c2cc3c([nH]2)cccc3OC
CACTVS 3.385COc1cccc2[nH]c(cc12)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)CO
FormulaC24 H34 N4 O6
NameN-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide;
N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form
ChEMBL
DrugBank
ZINC
PDB chain8j39 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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PDB8j39 Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF00835231
Resolution1.66 Å
Binding residue
(original residue number in PDB)
H41 F140 N142 C145 H163 H164 M165 E166 Q189 T190 A191
Binding residue
(residue number reindexed from 1)
H40 F139 N141 C144 H162 H163 M164 E165 Q188 T189 A190
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:8j39, PDBe:8j39, PDBj:8j39
PDBsum8j39
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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