Structure of PDB 5dpa Chain A Binding Site BS01

Receptor Information
>5dpa Chain A (length=181) Species: 39054 (Enterovirus A71) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MGPSLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWI
EHKLVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASD
ATLVINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGG
VVTSVGKVIGIHIGGNGRQGFCAGLKRSYFA
Ligand information
Ligand ID5F2
InChIInChI=1S/C22H29N3O5/c1-3-30-20(27)10-9-18(14-17-11-12-23-21(17)28)25-22(29)19(24-15(2)26)13-16-7-5-4-6-8-16/h4-10,17-19H,3,11-14H2,1-2H3,(H,23,28)(H,24,26)(H,25,29)/t17-,18+,19-/m0/s1
InChIKeyYYPCDXRHVHVVTA-OTWHNJEPSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(C)=O
OpenEye OEToolkits 1.9.2CCOC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)C
CACTVS 3.385CCOC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(C)=O
ACDLabs 12.01N2CCC(CC(/C=C\C(=O)OCC)NC(C(NC(C)=O)Cc1ccccc1)=O)C2=O
OpenEye OEToolkits 1.9.2CCOC(=O)C=CC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C
FormulaC22 H29 N3 O5
Nameethyl (2Z,4S)-4-[(N-acetyl-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
ChEMBL
DrugBank
ZINC
PDB chain5dpa Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5dpa Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71
Resolution2.06 Å
Binding residue
(original residue number in PDB)		R39 H40 E71 L127 S128 T142 K143 A144 G145 C147 H161 I162 G163 G164
Binding residue
(residue number reindexed from 1)		R40 H41 E72 L128 S129 T143 K144 A145 G146 C148 H162 I163 G164 G165
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.65,IC50=22.46uM
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dpa, PDBe:5dpa, PDBj:5dpa
PDBsum5dpa
PubMed26987809
UniProtA9XG43

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