Structure of PDB 8gxh Chain A Binding Site BS01

Receptor Information

>8gxh Chain A (length=303) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGV

Ligand information

• Ligand ID: 0AX
• InChI: InChI=1S/C34H42N4O6/c39-30(34(43)36-21-23-12-5-2-6-13-23)26(19-25-15-9-17-35-31(25)40)37-32(41)27(18-22-10-3-1-4-11-22)38-33(42)29-20-24-14-7-8-16-28(24)44-29/h2,5-8,12-14,16,20,22,25-27,30,39H,1,3-4,9-11,15,17-19,21H2,(H,35,40)(H,36,43)(H,37,41)(H,38,42)/t25-,26-,27-,30+/m0/s1
• InChIKey: QBWBVQMSMXVSSF-NJBJSMFESA-N
• SMILES:
  CACTVS 3.385: O[C@H]([C@H](C[C@@H]1CCCNC1=O)NC(=O)[C@H](CC2CCCCC2)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](CC3CCCCC3)NC(=O)c4cc5ccccc5o4)O
  CACTVS 3.385: O[CH]([CH](C[CH]1CCCNC1=O)NC(=O)[CH](CC2CCCCC2)NC(=O)c3oc4ccccc4c3)C(=O)NCc5ccccc5
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CNC(=O)C(C(CC2CCCNC2=O)NC(=O)C(CC3CCCCC3)NC(=O)c4cc5ccccc5o4)O
• Formula: C34 H42 N4 O6
• Name: N-[(2S)-3-cyclohexyl-1-oxidanylidene-1-[[(2S,3R)-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: 8gxh Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8gxh The crystal structure of SARS-CoV-2 main protease in complex with 14b
• Resolution: 1.59 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 G143 C145 H163 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H41 M49 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:8gxh, PDBe:8gxh, PDBj:8gxh
• PDBsum: 8gxh
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)