Structure of PDB 4dcd Chain A Binding Site BS01

Receptor Information

>4dcd Chain A (length=184) Species: 12081 (Human poliovirus 1 Mahoney)

HHHHGPGFDYAVAMAKRNIVTATTSKGEFTMLGVHDNVAILPTHASPGES
IVIDGKEVEILDAKALEDQAGTNLEITIITLKRNEKFRDIRPHIPTQITE
TNDGVLIVNTSKYPNMYVPVGAVTEQGYLNLGGRQTARTLMYNFPTRAGQ
CGGVITCTGKVIGMHVGGNGSHGFAAALKRSYFT

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: 4dcd Chain A Residue 202

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4dcd Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses.
• Resolution: 1.69 Å
• Binding residue (original residue number in PDB): H40 L127 G128 T142 R143 C147 H161 V162 G163 G164 N165
• Binding residue (residue number reindexed from 1): H44 L131 G132 T146 R147 C151 H165 V166 G167 G168 N169
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.75,IC50=1.77uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H40 E71 G145 C147
• Catalytic site (residue number reindexed from 1): H44 E75 G149 C151
• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  3.4.22.28: picornain 3C.
  3.4.22.29: picornain 2A.
  3.6.1.15: nucleoside-triphosphate phosphatase.

Gene Ontology

Molecular Function

• GO:0004197 cysteine-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:4dcd, PDBe:4dcd, PDBj:4dcd
• PDBsum: 4dcd
• PubMed: 22915796
• UniProt: P03300|POLG_POL1M Genome polyprotein