Structure of PDB 8dgy Chain A Binding Site BS01

Receptor Information

>8dgy Chain A (length=302) Species: 1335626 (Middle East respiratory syndrome-related coronavirus)

HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQ
LSDPNYDALLISMTNHSFSVQKHANLRVVGHAMQGTLLKLTVDVANPSTP
AYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSVG
YTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDKY
CSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSVD
MLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIMG
VV

Ligand information

• Ligand ID: S9U
• InChI: InChI=1S/C25H43N3O8S/c1-15(2)10-20(28-25(32)36-14-19-12-18(19)11-16-6-4-3-5-7-16)23(30)27-21(24(31)37(33,34)35)13-17-8-9-26-22(17)29/h15-21,24,31H,3-14H2,1-2H3,(H4-,26,27,28,29,30,32,33,34,35)/p+1/t17-,18+,19-,20-,21-,24-/m0/s1
• InChIKey: PBWNADCYPGWHEB-IKEPQGCXSA-O
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC[CH]1C[CH]1CC2CCCCC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S+](O)(O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC[C@@H]1C[C@H]1CC2CCCCC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](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)OCC2CC2CC3CCCCC3
  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)OC[C@@H]2C[C@H]2CC3CCCCC3
• Formula: C25 H44 N3 O8 S
• Name: [(1~{R},2~{R})-2-(cyclohexylmethyl)cyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate
• PDB chain: 8dgy Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8dgy Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): F143 G146 C148 H166 Q167 M168 E169 D190 Q192
• Binding residue (residue number reindexed from 1): F141 G144 C146 H164 Q165 M166 E167 D188 Q190
• 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.-
  3.6.4.12: 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:8dgy, PDBe:8dgy, PDBj:8dgy
• PDBsum: 8dgy
• PubMed: 36654747
• UniProt: K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab (Gene Name=rep)