Structure of PDB 5yia Chain A Binding Site BS01

Receptor Information
>5yia Chain A (length=328) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAG
CLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYK
FIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIEN
ALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHV
GNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNN
SKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFIL
GDPFMRKYFTVFDYDNQSVGIALAKKNL
Ligand information
Ligand ID8V9
InChIInChI=1S/C37H44N4O7S2/c1-37(2)33(35(47)40-31-26-12-8-7-11-24(26)19-29(31)43)41(21-50-37)36(48)32(45)27(17-22-9-5-4-6-10-22)39-34(46)28(20-49-3)38-30(44)18-23-13-15-25(42)16-14-23/h4-16,27-29,31-33,42-43,45H,17-21H2,1-3H3,(H,38,44)(H,39,46)(H,40,47)/t27-,28-,29+,31-,32-,33+/m0/s1
InChIKeyOONNUXMESNYHOP-ACUZRORGSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CSC[CH](NC(=O)Cc1ccc(O)cc1)C(=O)N[CH](Cc2ccccc2)[CH](O)C(=O)N3CSC(C)(C)[CH]3C(=O)N[CH]4[CH](O)Cc5ccccc45
OpenEye OEToolkits 2.0.6CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)C(CSC)NC(=O)Cc3ccc(cc3)O)O)C(=O)NC4c5ccccc5CC4O)C
OpenEye OEToolkits 2.0.6CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)[C@H](CSC)NC(=O)Cc3ccc(cc3)O)O)C(=O)N[C@H]4c5ccccc5C[C@H]4O)C
CACTVS 3.385CSC[C@H](NC(=O)Cc1ccc(O)cc1)C(=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
FormulaC37 H44 N4 O7 S2
Name
ChEMBLCHEMBL411608
DrugBank
ZINCZINC000028704133
PDB chain5yia Chain A Residue 401 [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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PDB5yia Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D36 G38 N78 Y79 V80 S81 L133 D216 G218 T219 S220 F296 I302
Binding residue
(residue number reindexed from 1)		D33 G35 N75 Y76 V77 S78 L130 D213 G215 T216 S217 F293 I299
Annotation score1
Binding affinityMOAD: Ki=3nM
PDBbind-CN: -logKd/Ki=5.52,Ki=3.0uM
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:5yia, PDBe:5yia, PDBj:5yia
PDBsum5yia
PubMed29943906
UniProtQ8I6V3|PLM2_PLAF7 Plasmepsin II (Gene Name=PMII)

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