Structure of PDB 5yib Chain A Binding Site BS01

Receptor Information
>5yib 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 ID8VC
InChIInChI=1S/C40H53N5O6S/c1-25-19-29(44(7)18-17-43(5)6)20-26(2)36(25)51-23-33(47)41-31(21-27-13-9-8-10-14-27)35(48)39(50)45-24-52-40(3,4)37(45)38(49)42-34-30-16-12-11-15-28(30)22-32(34)46/h8-16,19-20,31-32,34-35,37,46,48H,17-18,21-24H2,1-7H3,(H,41,47)(H,42,49)/t31-,32+,34-,35-,37+/m0/s1
InChIKeyIZETWNQXMIHLNU-IVJJLKHCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1cc(cc(c1OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NC4c5ccccc5CC4O)(C)C)O)C)N(C)CCN(C)C
CACTVS 3.385CN(C)CCN(C)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
CACTVS 3.385CN(C)CCN(C)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 2.0.6Cc1cc(cc(c1OCC(=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)N(C)CCN(C)C
FormulaC40 H53 N5 O6 S
Name
ChEMBLCHEMBL1208799
DrugBank
ZINCZINC000058599886
PDB chain5yib 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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PDB5yib Deciphering the mechanism of potent peptidomimetic inhibitors targeting plasmepsins - biochemical and structural insights.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		D36 G38 Y79 V80 S81 S134 D216 G218 T219 S220 I292 F296 I302
Binding residue
(residue number reindexed from 1)		D33 G35 Y76 V77 S78 S131 D213 G215 T216 S217 I289 F293 I299
Annotation score1
Binding affinityMOAD: Ki=3.3nM
PDBbind-CN: -logKd/Ki=5.48,Ki=3.3uM
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:5yib, PDBe:5yib, PDBj:5yib
PDBsum5yib
PubMed29943906
UniProtQ8I6V3|PLM2_PLAF7 Plasmepsin II (Gene Name=PMII)

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