Structure of PDB 5yid Chain A Binding Site BS01

Receptor Information
>5yid 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 IDK95
InChIInChI=1S/C37H44N4O6S2/c1-37(2)33(35(46)40-31-26-17-11-10-16-25(26)20-29(31)42)41(22-49-37)36(47)32(44)27(18-23-12-6-4-7-13-23)39-34(45)28(21-48-3)38-30(43)19-24-14-8-5-9-15-24/h4-17,27-29,31-33,42,44H,18-22H2,1-3H3,(H,38,43)(H,39,45)(H,40,46)/t27-,28-,29+,31-,32-,33+/m0/s1
InChIKeyFCTXMHJXDHGIIN-ACUZRORGSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CSC[C@H](NC(=O)Cc1ccccc1)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
CACTVS 3.370CSC[CH](NC(=O)Cc1ccccc1)C(=O)N[CH](Cc2ccccc2)[CH](O)C(=O)N3CSC(C)(C)[CH]3C(=O)N[CH]4[CH](O)Cc5ccccc45
OpenEye OEToolkits 1.7.0CC1(C(N(CS1)C(=O)C(C(Cc2ccccc2)NC(=O)C(CSC)NC(=O)Cc3ccccc3)O)C(=O)NC4c5ccccc5CC4O)C
OpenEye OEToolkits 1.7.0CC1([C@H](N(CS1)C(=O)[C@H]([C@H](Cc2ccccc2)NC(=O)[C@H](CSC)NC(=O)Cc3ccccc3)O)C(=O)N[C@H]4c5ccccc5C[C@H]4O)C
ACDLabs 12.01O=C(NC2c1ccccc1CC2O)C5N(C(=O)C(O)C(NC(=O)C(NC(=O)Cc3ccccc3)CSC)Cc4ccccc4)CSC5(C)C
FormulaC37 H44 N4 O6 S2
Name(4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-{[S-methyl-N-(phenylacetyl)-L-cysteinyl]ami no}-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
KNI-10395
ChEMBLCHEMBL411610
DrugBank
ZINCZINC000028704146
PDB chain5yid 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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PDB5yid 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 G218 T219 S220 L294 F296 I302
Binding residue
(residue number reindexed from 1)
D32 G34 Y75 V76 S77 I121 G214 T215 S216 L290 F292 I298
Annotation score1
Binding affinityMOAD: Ki=4nM
PDBbind-CN: -logKd/Ki=5.40,Ki=4.0uM
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:5yid, PDBe:5yid, PDBj:5yid
PDBsum5yid
PubMed29943906
UniProtQ8I6V3|PLM2_PLAF7 Plasmepsin II (Gene Name=PMII)

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