Structure of PDB 7s75 Chain A Binding Site BS01

Receptor Information

>7s75 Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLAGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: 8I7
• InChI: InChI=1S/C26H44N4O5/c1-14(2)10-18(32)29-21(25(3,4)5)24(35)30-12-17-19(26(17,6)7)20(30)23(34)28-16(13-31)11-15-8-9-27-22(15)33/h14-17,19-21,31H,8-13H2,1-7H3,(H,27,33)(H,28,34)(H,29,32)/t15-,16-,17-,19-,20-,21+/m0/s1
• InChIKey: YJDABKUOTKRKDF-RZCQQDKOSA-N
• SMILES:
  CACTVS 3.385: CC(C)CC(=O)N[C@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@H](CO)C[C@@H]3CCNC3=O)C2(C)C)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(C)CC(=O)N[C@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)CO)C2(C)C)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(C)CC(=O)NC(C(=O)N1CC2C(C1C(=O)NC(CC3CCNC3=O)CO)C2(C)C)C(C)(C)C
  CACTVS 3.385: CC(C)CC(=O)N[CH](C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](CO)C[CH]3CCNC3=O)C2(C)C)C(C)(C)C
  ACDLabs 12.01: CC1(C)C2C(C(=O)NC(CC3CCNC3=O)CO)N(CC21)C(=O)C(NC(=O)CC(C)C)C(C)(C)C
• Formula: C26 H44 N4 O5
• Name: (1R,2S,5S)-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(3-methylbutanoyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 7s75 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7s75 A systematic exploration of boceprevir-based main protease inhibitors as SARS-CoV-2 antivirals.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 Q189 Q192
• Binding residue (residue number reindexed from 1): H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 Q189 Q192
• 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:7s75, PDBe:7s75, PDBj:7s75
• PDBsum: 7s75
• PubMed: 35839690
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)