Structure of PDB 5wkj Chain A Binding Site BS02

Receptor Information

>5wkj Chain A (length=302) Species: 1335626 (Middle East respiratory syndrome-related coronavirus)

HHSGLVKMSHPSGDVEACMVQVTCGSMTLNGLWLDNTVWCPRHVMCPADQ
LSDPNYDALLISMTNHSFSVQKHIANLRVVGHAMQGTLLKLTVDVANPST
PAYTFTTVKPGAAFSVLACYNGRPTGTFTVVMRPNYTIKGSFLCGSCGSV
GYTKEGSVINFCYMHQMELANGTHTGSAFDGTMYGAFMDKQVHQVQLTDK
YCSVNVVAWLYAAILNGCAWFVKPNRTSVVSFNEWALANQFTEFVGTQSV
DMLAVKTGVAIEQLLYAIQQLYTGFQGKQILGSTMLEDEFTPEDVNMQIM
GV

Ligand information

• Ligand ID: K36
• InChI: InChI=1S/C21H31N3O8S/c1-13(2)10-16(24-21(28)32-12-14-6-4-3-5-7-14)19(26)23-17(20(27)33(29,30)31)11-15-8-9-22-18(15)25/h3-7,13,15-17,20,27H,8-12H2,1-2H3,(H,22,25)(H,23,26)(H,24,28)(H,29,30,31)/t15-,16-,17-,20?/m0/s1
• InChIKey: BSPZFJDYQHDZNR-HTCLRFROSA-N
• SMILES:
  ACDLabs 12.01: O=C(OCc1ccccc1)NC(C(=O)NC(CC2C(=O)NCC2)C(O)S(=O)(=O)O)CC(C)C
  CACTVS 3.370: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O
  CACTVS 3.370: CC(C)C[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  OpenEye OEToolkits 1.7.6: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](O)S(=O)(=O)O)NC(=O)OCc2ccccc2
  OpenEye OEToolkits 1.7.6: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccccc2
• Formula: C21 H31 N3 O8 S
• Name: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid;
  GC376
• ChEMBL: CHEMBL3559293
• PDB chain: 5wkj Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5wkj Structure-guided design of potent and permeable inhibitors of MERS coronavirus 3CL protease that utilize a piperidine moiety as a novel design element.
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): H41 F143 G146 C148 H166 Q167 M168 E169 Q192
• Binding residue (residue number reindexed from 1): H43 F142 G145 C147 H165 Q166 M167 E168 Q191
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.50: mRNA guanylyltransferase.
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:5wkj, PDBe:5wkj, PDBj:5wkj
• PDBsum: 5wkj
• PubMed: 29544147
• UniProt: K9N638|R1A_MERS1 Replicase polyprotein 1a (Gene Name=1a)