Structure of PDB 8gxg Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG

Ligand information

• Ligand ID: 06Q
• InChI: InChI=1S/C34H35FN4O6/c35-25-14-12-21(13-15-25)17-27(39-33(43)29-19-23-9-4-5-11-28(23)45-29)32(42)38-26(18-24-10-6-16-36-31(24)41)30(40)34(44)37-20-22-7-2-1-3-8-22/h1-5,7-9,11-15,19,24,26-27,30,40H,6,10,16-18,20H2,(H,36,41)(H,37,44)(H,38,42)(H,39,43)/t24-,26-,27-,30-/m0/s1
• InChIKey: RXCWWLZLSPDOKP-LRVPPHGTSA-N
• SMILES:
  CACTVS 3.385: O[C@@H]([C@H](C[C@@H]1CCCNC1=O)NC(=O)[C@H](Cc2ccc(F)cc2)NC(=O)c3oc4ccccc4c3)C(=O)NCc5ccccc5
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CNC(=O)C(C(CC2CCCNC2=O)NC(=O)C(Cc3ccc(cc3)F)NC(=O)c4cc5ccccc5o4)O
  CACTVS 3.385: O[CH]([CH](C[CH]1CCCNC1=O)NC(=O)[CH](Cc2ccc(F)cc2)NC(=O)c3oc4ccccc4c3)C(=O)NCc5ccccc5
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CNC(=O)[C@H]([C@H](C[C@@H]2CCCNC2=O)NC(=O)[C@H](Cc3ccc(cc3)F)NC(=O)c4cc5ccccc5o4)O
• Formula: C34 H35 F N4 O6
• Name: N-[(2S)-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2S,3S)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepiperidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-1-benzofuran-2-carboxamide
• PDB chain: 8gxg Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gxg The crystal structure of SARS-CoV-2 main protease in complex with 14a
• Resolution: 1.69 Å
• Binding residue (original residue number in PDB): T25 H41 M49 F140 N142 G143 C145 H163 M165 E166 D187 R188 Q189
• Binding residue (residue number reindexed from 1): T25 H41 M49 F140 N142 G143 C145 H163 M165 E166 D187 R188 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:8gxg, PDBe:8gxg, PDBj:8gxg
• PDBsum: 8gxg
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)