Structure of PDB 7qka Chain A Binding Site BS01

Receptor Information

>7qka Chain A (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: UED
• InChI: InChI=1S/C21H31N3O5/c1-14(2)10-18(24-21(28)29-13-15-6-4-3-5-7-15)20(27)23-17(12-25)11-16-8-9-22-19(16)26/h3-7,14,16-18,25H,8-13H2,1-2H3,(H,22,26)(H,23,27)(H,24,28)/t16-,17-,18-/m0/s1
• InChIKey: JUCVXDDMQHPCKT-BZSNNMDCSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)CO)NC(=O)OCc2ccccc2
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](CO)C[CH]2CCNC2=O
  ACDLabs 12.01: C(OC(=O)NC(C(NC(CO)CC1C(NCC1)=O)=O)CC(C)C)c2ccccc2
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)CO)NC(=O)OCc2ccccc2
• Formula: C21 H31 N3 O5
• Name: N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide;
  GC373 bound form, GC376 bound form
• ZINC: ZINC000072178988
• PDB chain: 7qka Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qka Towards automated crystallographic structure refinement with phenix.refine.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H41 F140 L141 N142 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H41 F140 L141 N142 C145 H163 H164 M165 E166 D187 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:7qka, PDBe:7qka, PDBj:7qka
• PDBsum: 7qka
• PubMed: 37853179
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)