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Structure of PDB 9arq Chain A Binding Site BS01

Receptor Information

>9arq Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: T2L
• InChI: InChI=1S/C30H37F4N5O5S/c1-28(2,3)22(38-27(44)30(32,33)34)26(43)39-12-14-18(29(14,4)5)20(39)24(42)36-16(11-13-9-10-35-23(13)41)21(40)25-37-19-15(31)7-6-8-17(19)45-25/h6-8,13-14,16,18,20-22,40H,9-12H2,1-5H3,(H,35,41)(H,36,42)(H,38,44)/t13-,14-,16-,18-,20-,21-,22+/m0/s1
• InChIKey: HZJVVPOOURAASY-SWSSSNQJSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](c4nc5c(cccc5s4)F)O)C
  ACDLabs 12.01: FC(F)(F)C(=O)NC(C(=O)N1CC2C(C1C(=O)NC(CC1CCNC1=O)C(O)c1nc3c(F)cccc3s1)C2(C)C)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C(c4nc5c(cccc5s4)F)O)C
  CACTVS 3.385: CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)c4sc5cccc(F)c5n4)C2(C)C
  CACTVS 3.385: CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)c4sc5cccc(F)c5n4)C2(C)C
• Formula: C30 H37 F4 N5 O5 S
• Name: (1R,2S,5S)-N-{(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 9arq Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 9arq Structural and virologic mechanism of emergence of main protease inhibitor-resistance in SARS-CoV-2 as selected with main protease inhibitors
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): T25 H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): T25 H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 Q189
• Annotation score: 1

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

External links

• PDB: RCSB:9arq, PDBe:9arq, PDBj:9arq
• PDBsum: 9arq
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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