Structure of PDB 7t4a Chain A Binding Site BS02

Receptor Information

>7t4a Chain A (length=292) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICLNPNYEDL
LIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQ
PGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV
SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAW
LYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQT
GIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQ

Ligand information

• Ligand ID: EO6
• InChI: InChI=1S/C23H37N5O8S/c1-14(2)9-17(27-22(32)36-16-11-23(12-16)4-7-28(13-24)8-5-23)20(30)26-18(21(31)37(33,34)35)10-15-3-6-25-19(15)29/h14-18,21,31H,3-12H2,1-2H3,(H,25,29)(H,26,30)(H,27,32)(H,33,34,35)/t15-,17-,18-,21+/m0/s1
• InChIKey: CSWBWWIUTWLAOZ-QUJKESNLSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC1CC2(CCN(CC2)C#N)C1)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC1CC2(CCN(CC2)C#N)C1)C(=O)N[CH](C[CH]3CCNC3=O)[CH](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)C#N
  ACDLabs 12.01: O=C1NCCC1CC(NC(=O)C(CC(C)C)NC(=O)OC1CC2(CCN(CC2)C#N)C1)C(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)C#N
• Formula: C23 H37 N5 O8 S
• Name: (1R,2S)-2-[(N-{[(7-cyano-7-azaspiro[3.5]nonan-2-yl)oxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 7t4a Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7t4a Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H41 F140 L141 N142 C145 H163 H164 M165 E166 L167 D187 Q189
• Binding residue (residue number reindexed from 1): H39 F133 L134 N135 C138 H156 H157 M158 E159 L160 D180 Q182
• 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:7t4a, PDBe:7t4a, PDBj:7t4a
• PDBsum: 7t4a
• PubMed: 35638577
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)