Structure of PDB 7t49 Chain A Binding Site BS01

Receptor Information

>7t49 Chain A (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: FV5
• InChI: InChI=1S/C23H40N4O10S2/c1-14(2)10-17(20(29)25-18(21(30)39(34,35)36)11-15-4-7-24-19(15)28)26-22(31)37-16-12-23(13-16)5-8-27(9-6-23)38(3,32)33/h14-18,21,30H,4-13H2,1-3H3,(H,24,28)(H,25,29)(H,26,31)(H,34,35,36)/t15-,17-,18-,21+/m0/s1
• InChIKey: DXHKTWBJEAVWSD-QUJKESNLSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC1CC2(CCN(CC2)[S](C)(=O)=O)C1)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CC3(C2)CCN(CC3)S(=O)(=O)C
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC1CC2(CCN(CC2)[S](C)(=O)=O)C1)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OC2CC3(C2)CCN(CC3)S(=O)(=O)C
  ACDLabs 12.01: O=C1NCCC1CC(NC(=O)C(CC(C)C)NC(=O)OC1CC2(CCN(CC2)S(C)(=O)=O)C1)C(O)S(=O)(=O)O
• Formula: C23 H40 N4 O10 S2
• Name: (1R,2S)-1-hydroxy-2-{[N-({[7-(methanesulfonyl)-7-azaspiro[3.5]nonan-2-yl]oxy}carbonyl)-L-leucyl]amino}-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 7t49 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7t49 Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): H41 F140 N142 C145 H163 H164 M165 E166 P168 D187 Q189
• Binding residue (residue number reindexed from 1): H39 F138 N140 C143 H161 H162 M163 E164 P166 D185 Q187
• 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:7t49, PDBe:7t49, PDBj:7t49
• PDBsum: 7t49
• PubMed: 35638577
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)