Structure of PDB 8gxi Chain A Binding Site BS01

Receptor Information

>8gxi Chain A (length=302) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG

Ligand information

• Ligand ID: 0BO
• InChI: InChI=1S/C30H40N4O6/c35-26(30(39)32-21-12-13-21)22(16-20-10-6-14-31-27(20)36)33-28(37)23(15-18-7-2-1-3-8-18)34-29(38)25-17-19-9-4-5-11-24(19)40-25/h4-5,9,11,17-18,20-23,26,35H,1-3,6-8,10,12-16H2,(H,31,36)(H,32,39)(H,33,37)(H,34,38)/t20-,22-,23-,26+/m0/s1
• InChIKey: FLHCDUBGBDAQOK-PETUGJSASA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc2c(c1)cc(o2)C(=O)NC(CC3CCCCC3)C(=O)NC(CC4CCCNC4=O)C(C(=O)NC5CC5)O
  OpenEye OEToolkits 2.0.7: c1ccc2c(c1)cc(o2)C(=O)N[C@@H](CC3CCCCC3)C(=O)N[C@@H](C[C@@H]4CCCNC4=O)[C@H](C(=O)NC5CC5)O
  CACTVS 3.385: O[CH]([CH](C[CH]1CCCNC1=O)NC(=O)[CH](CC2CCCCC2)NC(=O)c3oc4ccccc4c3)C(=O)NC5CC5
  CACTVS 3.385: O[C@H]([C@H](C[C@@H]1CCCNC1=O)NC(=O)[C@H](CC2CCCCC2)NC(=O)c3oc4ccccc4c3)C(=O)NC5CC5
• Formula: C30 H40 N4 O6
• Name: N-[(2S)-3-cyclohexyl-1-[[(2S,3R)-4-(cyclopropylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-1-benzofuran-2-carboxamide
• PDB chain: 8gxi Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gxi The crystal structure of SARS-CoV-2 main protease in complex with 14c
• Resolution: 1.69 Å
• Binding residue (original residue number in PDB): T26 H41 F140 N142 G143 C145 H163 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): T26 H41 F140 N142 G143 C145 H163 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:8gxi, PDBe:8gxi, PDBj:8gxi
• PDBsum: 8gxi
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)