Structure of PDB 5dp3 Chain A Binding Site BS01

Receptor Information

>5dp3 Chain A (length=181) Species: 39054 (Enterovirus A71)

MGPSLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWI
EHKLVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASD
ATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGG
VVTSVGKVIGIHIGGNGRQGFCAGLKRSYFA

Ligand information

• Ligand ID: 5GH
• InChI: InChI=1S/C20H26N2O4/c1-2-26-19(24)11-9-17(14-16-12-13-21-20(16)25)22-18(23)10-8-15-6-4-3-5-7-15/h3-7,9,11,16-17H,2,8,10,12-14H2,1H3,(H,21,25)(H,22,23)/b11-9-/t16-,17+/m0/s1
• InChIKey: QZQFSCIYJVNTSL-UMYABFQBSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CCOC(=O)C=CC(CC1CCNC1=O)NC(=O)CCc2ccccc2
  CACTVS 3.385: CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)CCc2ccccc2
  ACDLabs 12.01: N2CCC(CC(NC(CCc1ccccc1)=O)[C@H]=[C@H]C(OCC)=O)C2=O
  CACTVS 3.385: CCOC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)CCc2ccccc2
  OpenEye OEToolkits 1.9.2: CCOC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)CCc2ccccc2
• Formula: C20 H26 N2 O4
• Name: ethyl (4S)-5-[(3S)-2-oxopyrrolidin-3-yl]-4-[(3-phenylpropanoyl)amino]pent-2-enoate
• ZINC: ZINC000584904871
• PDB chain: 5dp3 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dp3 Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): H40 K143 A144 C147 G163 G164
• Binding residue (residue number reindexed from 1): H41 K144 A145 C148 G164 G165
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H40 E71 G145 C147
• Catalytic site (residue number reindexed from 1): H41 E72 G146 C148
• 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:5dp3, PDBe:5dp3, PDBj:5dp3
• PDBsum: 5dp3
• PubMed: 26987809
• UniProt: A9XG43