Structure of PDB 8e6e Chain A Binding Site BS01

Receptor Information

>8e6e Chain A (length=306) Species: 1335626 (Middle East respiratory syndrome-related coronavirus)

HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQ
LSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVAN
PSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSC
GSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQL
TDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGT
QSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNM
QIMGVV

Ligand information

• Ligand ID: UUR
• InChI: InChI=1S/C22H33N3O8S2/c1-14(2)12-17(25-22(29)33-10-11-34-16-6-4-3-5-7-16)20(27)24-18(21(28)35(30,31)32)13-15-8-9-23-19(15)26/h3-7,14-15,17-18,21,28H,8-13H2,1-2H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t15-,17-,18-,21-/m0/s1
• InChIKey: AUIXPEVQDXBTHO-DBSRCYSRSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCCSc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](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)OCCSc2ccccc2
  ACDLabs 12.01: CC(C)CC(NC(=O)OCCSc1ccccc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
  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)OCCSc2ccccc2
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCCSc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O
• Formula: C22 H33 N3 O8 S2
• Name: 2-phenylsulfanylethyl ~{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: 8e6e Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e6e Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)
• Resolution: 1.5 Å
• Binding residue (original residue number in PDB): F143 C145 G146 C148 H166 Q167 M168 E169 L170 D190 Q192 V193 H194 Q195
• Binding residue (residue number reindexed from 1): F145 C147 G148 C150 H168 Q169 M170 E171 L172 D192 Q194 V195 H196 Q197
• 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:8e6e, PDBe:8e6e, PDBj:8e6e
• PDBsum: 8e6e
• PubMed: 37080108
• UniProt: K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab (Gene Name=rep)