Structure of PDB 8ups Chain A Binding Site BS01

Receptor Information

>8ups Chain A (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: I70
• InChI: InChI=1S/C27H46N6O6/c1-25(2,3)19(31-24(39)32-26(4,5)6)23(38)33-12-14-16(27(14,7)8)17(33)22(37)30-15(18(34)20(28)35)11-13-9-10-29-21(13)36/h13-19,34H,9-12H2,1-8H3,(H2,28,35)(H,29,36)(H,30,37)(H2,31,32,39)/t13-,14-,15-,16-,17-,18+,19+/m0/s1
• InChIKey: PGHPGMLPXLZINT-UYYZUGKPSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)NC(C)(C)C)C(=O)NC(CC3CCNC3=O)C(C(=O)N)O)C
  ACDLabs 12.01: CC1(C)C2C(C(=O)NC(CC3CCNC3=O)C(O)C(N)=O)N(CC21)C(=O)C(NC(=O)NC(C)(C)C)C(C)(C)C
  CACTVS 3.385: CC(C)(C)NC(=O)N[CH](C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)C(N)=O)C2(C)C)C(C)(C)C
  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)NC(C)(C)C)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](C(=O)N)O)C
  CACTVS 3.385: CC(C)(C)NC(=O)N[C@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)C(N)=O)C2(C)C)C(C)(C)C
• Formula: C27 H46 N6 O6
• Name: (1R,2S,5S)-N-{(2S,3R)-4-amino-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 8ups Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ups Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
• Resolution: 2.44 Å
• Binding residue (original residue number in PDB): H41 F140 N142 G143 C145 H163 H164 M165 E166 L167 D187 R188 Q189 T190 Q192
• Binding residue (residue number reindexed from 1): H41 F140 N142 G143 C145 H163 H164 M165 E166 L167 D187 R188 Q189 T190 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:8ups, PDBe:8ups, PDBj:8ups
• PDBsum: 8ups
• PubMed: 38365209
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)