Structure of PDB 4y6m Chain A Binding Site BS01

Receptor Information
>4y6m Chain A (length=329) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTA
GCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPY
KFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIE
NALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAH
VGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCN
NSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFI
LGDPFMRKYFTVFDYDNHSVGIALAKKNL
Ligand information
Ligand ID48Q
InChIInChI=1S/C39H52N4O4/c1-6-19-43(20-7-2)38(46)31-24-30(25-33(26-31)42-21-12-9-13-22-42)37(45)41-35(23-29-15-10-8-11-16-29)36(44)28-40-39(3,4)32-17-14-18-34(27-32)47-5/h8,10-11,14-18,23-27,36,40,44H,6-7,9,12-13,19-22,28H2,1-5H3,(H,41,45)/b35-23-/t36-/m1/s1
InChIKeyUCBMZABMPAPJRC-LMOGZCTNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N\C(=C/c2ccccc2)[C@H](O)CNC(C)(C)c3cccc(OC)c3)N4CCCCC4
OpenEye OEToolkits 2.0.4CCCN(CCC)C(=O)c1cc(cc(c1)N2CCCCC2)C(=O)NC(=Cc3ccccc3)C(CNC(C)(C)c4cccc(c4)OC)O
CACTVS 3.385CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(=Cc2ccccc2)[CH](O)CNC(C)(C)c3cccc(OC)c3)N4CCCCC4
OpenEye OEToolkits 2.0.4CCCN(CCC)C(=O)c1cc(cc(c1)N2CCCCC2)C(=O)N/C(=C\c3ccccc3)/[C@@H](CNC(C)(C)c4cccc(c4)OC)O
FormulaC39 H52 N4 O4
Name~{N}1-[(~{Z},3~{R})-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-but-1-en-2-yl]-5-piperidin-1-yl-~{N}3,~{N}3-dipropyl-benzene-1,3-dicarboxamide
ChEMBL
DrugBank
ZINCZINC000263621082
PDB chain4y6m Chain A Residue 501 [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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PDB4y6m Structures of plasmepsin II from Plasmodium falciparum in complex with two hydroxyethylamine-based inhibitors.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		I32 D34 G36 V78 T114 I123 Y192 D214 G216 T217 S218 I300
Binding residue
(residue number reindexed from 1)		I32 D34 G36 V78 T114 I123 Y192 D214 G216 T217 S218 I300
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.15,IC50=0.07uM
Enzymatic activity
Catalytic site (original residue number in PDB) D34 S37 N39 W41 Y77 D214 T217
Catalytic site (residue number reindexed from 1) D34 S37 N39 W41 Y77 D214 T217
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:4y6m, PDBe:4y6m, PDBj:4y6m
PDBsum4y6m
PubMed26625296
UniProtP46925|PLM2_PLAFX Plasmepsin II (Gene Name=PMII)

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