Structure of PDB 8e6b Chain A Binding Site BS02

Receptor Information

>8e6b Chain A (length=306) Species: 1335626 (Middle East respiratory syndrome-related coronavirus)

HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQ
LSDPNYDALLISMTNHSFSVQKHIGAPANLRVVGHAMQGTLLKLTVDVAN
PSTPAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSC
GSVGYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQL
TDKYCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGT
QSVDMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNM
QIMGVV

Ligand information

• Ligand ID: UO9
• InChI: InChI=1S/C24H37N3O9S2/c1-15(2)12-18(27-23(31)36-14-24(3,4)37(32)17-8-6-5-7-9-17)21(29)26-19(22(30)38(33,34)35)13-16-10-11-25-20(16)28/h5-9,15-16,18-19,22,30H,10-14H2,1-4H3,(H,25,28)(H,26,29)(H,27,31)(H,33,34,35)/t16-,18-,19-,22+,37-/m0/s1
• InChIKey: SNFBJKJTJOFDKW-NRANLDPGSA-N
• SMILES:
  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)OCC(C)(C)S(=O)c2ccccc2
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCC(C)(C)[S](=O)c1ccccc1)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)OCC(C)(C)S(=O)c2ccccc2
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCC(C)(C)[S@@](=O)c1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  ACDLabs 12.01: CC(C)CC(NC(=O)OCC(C)(C)S(=O)c1ccccc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
• Formula: C24 H37 N3 O9 S2
• Name: (2~{S})-2-[[(2~{S})-4-methyl-2-[[2-methyl-2-[oxidanyl(phenyl)-$l^{3}-sulfanyl]propoxy]carbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 8e6b Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e6b 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: 1.55 Å
• Binding residue (original residue number in PDB): F143 C145 C148 H166 Q167 M168 E169 L170 A171 D190 Q192 V193 H194
• Binding residue (residue number reindexed from 1): F145 C147 C150 H168 Q169 M170 E171 L172 A173 D192 Q194 V195 H196
• 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:8e6b, PDBe:8e6b, PDBj:8e6b
• PDBsum: 8e6b
• PubMed: 37080108
• UniProt: K9N7C7|R1AB_MERS1 Replicase polyprotein 1ab (Gene Name=rep)