Structure of PDB 5dp6 Chain A Binding Site BS01

Receptor Information
>5dp6 Chain A (length=178) Species: 39054 (Enterovirus A71) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLDFALSLLRRNVRQVQTDQGHFTMLGVRDRLAVLPRHSQPGKTIWIEHK
LVNILDAVELVDEQGVNLELTLITLDTNEKFRDITKFIPENISTASDATL
VINTEHMPSMFVPVGDVVQYGFLNLSGKPTHRTMMYNFPTKAGQCGGVVT
SVGKVIGIHIGGNGRQGFCAGLKRSYFA
Ligand information
Ligand ID5EB
InChIInChI=1S/C26H35N3O5/c1-2-34-24(31)13-11-21(17-20-14-15-27-25(20)32)28-26(33)22(16-19-6-4-3-5-7-19)29-23(30)12-10-18-8-9-18/h3-7,11,13,18,20-22H,2,8-10,12,14-17H2,1H3,(H,27,32)(H,28,33)(H,29,30)/t20-,21+,22-/m0/s1
InChIKeyQRJJXRNUFIJDHO-BDTNDASRSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCOC(=O)C=C[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)CCC3CC3
CACTVS 3.385CCOC(=O)\C=C/[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)CCC3CC3
ACDLabs 12.01C(Cc1ccccc1)(C(=O)NC(\C=C/C(=O)OCC)CC2C(NCC2)=O)NC(=O)CCC3CC3
OpenEye OEToolkits 1.9.2CCOC(=O)C=C[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)CCC3CC3
OpenEye OEToolkits 1.9.2CCOC(=O)C=CC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)CCC3CC3
FormulaC26 H35 N3 O5
Nameethyl (2Z,4S)-4-{[N-(3-cyclopropylpropanoyl)-L-phenylalanyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate
ChEMBL
DrugBank
ZINC
PDB chain5dp6 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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PDB5dp6 Fragment-wise design of inhibitors to 3C proteinase from enterovirus 71
Resolution3.01 Å
Binding residue
(original residue number in PDB)		H40 L127 S128 T142 K143 G145 C147 I162 G164
Binding residue
(residue number reindexed from 1)		H38 L125 S126 T140 K141 G143 C145 I160 G162
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.83,IC50=14.71uM
Enzymatic activity
Catalytic site (original residue number in PDB) H40 E71 G145 C147
Catalytic site (residue number reindexed from 1) H38 E69 G143 C145
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:5dp6, PDBe:5dp6, PDBj:5dp6
PDBsum5dp6
PubMed26987809
UniProtA9XG43

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