Structure of PDB 8f44 Chain A Binding Site BS01

Receptor Information
>8f44 Chain A (length=300) 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
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
Ligand information
Ligand IDXFF
InChIInChI=1S/C24H37N3O8S2/c1-15(2)12-18(27-23(31)35-14-24(3,4)36-17-8-6-5-7-9-17)21(29)26-19(22(30)37(32,33)34)13-16-10-11-25-20(16)28/h5-9,15-16,18-19,22,30H,10-14H2,1-4H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t16-,18-,19-,22-/m0/s1
InChIKeyAGWHKDXHVADVIY-FUOQNJDISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC(C)(C)Sc2ccccc2
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](O)S(=O)(=O)O)NC(=O)OCC(C)(C)Sc2ccccc2
CACTVS 3.385CC(C)C[C@H](NC(=O)OCC(C)(C)Sc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O
CACTVS 3.385CC(C)C[CH](NC(=O)OCC(C)(C)Sc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
ACDLabs 12.01CC(C)CC(NC(=O)OCC(C)(C)Sc1ccccc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
FormulaC24 H37 N3 O8 S2
Name(2-methyl-2-phenylsulfanyl-propyl) ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain8f44 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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PDB8f44 Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)
Resolution1.65 Å
Binding residue
(original residue number in PDB)
F140 G143 C145 H163 H164 M165 E166 P168 Q189 T190
Binding residue
(residue number reindexed from 1)
F139 G142 C144 H162 H163 M164 E165 P167 Q188 T189
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:8f44, PDBe:8f44, PDBj:8f44
PDBsum8f44
PubMed37080108
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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