Structure of PDB 5yie Chain A Binding Site BS01

Receptor Information
>5yie Chain A (length=327) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGC
LTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKF
IEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENA
LFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVG
NIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNS
KLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILG
DPFMRKYFTVFDYDNQSVGIALAKKNL
Ligand information
Ligand ID8VF
InChIInChI=1S/C39H51N5O6S/c1-6-43(17-16-40)28-18-24(2)35(25(3)19-28)50-22-32(46)41-30(20-26-12-8-7-9-13-26)34(47)38(49)44-23-51-39(4,5)36(44)37(48)42-33-29-15-11-10-14-27(29)21-31(33)45/h7-15,18-19,30-31,33-34,36,45,47H,6,16-17,20-23,40H2,1-5H3,(H,41,46)(H,42,48)/t30-,31+,33-,34-,36+/m0/s1
InChIKeyQVEVEYWLPLMZQY-SQKWSBCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCN(CCN)c1cc(c(c(c1)C)OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NC4c5ccccc5CC4O)(C)C)O)C
CACTVS 3.385CCN(CCN)c1cc(C)c(OCC(=O)N[CH](Cc2ccccc2)[CH](O)C(=O)N3CSC(C)(C)[CH]3C(=O)N[CH]4[CH](O)Cc5ccccc45)c(C)c1
OpenEye OEToolkits 2.0.6CCN(CCN)c1cc(c(c(c1)C)OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)N[C@H]4c5ccccc5C[C@H]4O)(C)C)O)C
CACTVS 3.385CCN(CCN)c1cc(C)c(OCC(=O)N[C@@H](Cc2ccccc2)[C@H](O)C(=O)N3CSC(C)(C)[C@H]3C(=O)N[C@@H]4[C@H](O)Cc5ccccc45)c(C)c1
FormulaC39 H51 N5 O6 S
Name
ChEMBLCHEMBL1209499
DrugBank
ZINCZINC000058651292
PDB chain5yie Chain A Residue 403 [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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PDB5yie Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D36 G38 Y79 V80 S81 I125 L133 I135 D216 G218 T219 S220 L294 F296 I302
Binding residue
(residue number reindexed from 1)		D32 G34 Y75 V76 S77 I121 L129 I131 D212 G214 T215 S216 L290 F292 I298
Annotation score1
Binding affinityMOAD: Ki=5.6nM
PDBbind-CN: -logKd/Ki=5.25,Ki=5.6uM
Enzymatic activity
Enzyme Commision number 3.4.23.39: plasmepsin II.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:5yie, PDBe:5yie, PDBj:5yie
PDBsum5yie
PubMed29943906
UniProtQ8I6V3|PLM2_PLAF7 Plasmepsin II (Gene Name=PMII)

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