Structure of PDB 5dp9 Chain A Binding Site BS01

Receptor Information
>5dp9 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 ID5EX
InChIInChI=1S/C27H36N4O6/c1-2-37-23(32)12-11-21(16-20-13-14-28-24(20)33)30-25(34)22(15-18-7-4-3-5-8-18)31-27(36)26(35)29-17-19-9-6-10-19/h3-5,7-8,11-12,19-22H,2,6,9-10,13-17H2,1H3,(H,28,33)(H,29,35)(H,30,34)(H,31,36)/t20-,21+,22-/m0/s1
InChIKeyJXIYUFBHNQDFQS-BDTNDASRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCOC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
OpenEye OEToolkits 1.9.2CCOC(=O)C=CC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
ACDLabs 12.01C1(CCC1)CNC(=O)C(NC(Cc2ccccc2)C(NC(CC3CCNC3=O)[C@H]=[C@H]C(OCC)=O)=O)=O
CACTVS 3.385CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
CACTVS 3.385CCOC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)C(=O)NCC3CCC3
FormulaC27 H36 N4 O6
Nameethyl (2Z,4S)-4-[(N-{[(cyclobutylmethyl)amino](oxo)acetyl}-L-phenylalanyl)amino]-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
ChEMBL
DrugBank
ZINC
PDB chain5dp9 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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PDB5dp9 Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H40 E71 L125 N126 L127 S128 T142 K143 A144 C147 H161 I162 G163 G164
Binding residue
(residue number reindexed from 1)		H41 E72 L126 N127 L128 S129 T143 K144 A145 C148 H162 I163 G164 G165
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.08,IC50=0.84uM
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:5dp9, PDBe:5dp9, PDBj:5dp9
PDBsum5dp9
PubMed26987809
UniProtA9XG43

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