Structure of PDB 4cku Chain E Binding Site BS01

Receptor Information
>4cku Chain E (length=322) Species: 5833 (Plasmodium falciparum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAG
CLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYK
FIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIEN
ALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHV
GNISLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNN
SKLPTFEFTSENGKYTLEPEYYLQHGLCMLNIIGLDFPVPTFILGDPFMR
KYFTVFDYDNHSVGIALAKKNL
Ligand information
Ligand IDP2F
InChIInChI=1S/C38H52N4O6S/c1-6-18-41(19-7-2)37(45)30-23-29(24-32(25-30)42-20-11-12-21-49(42,46)47)36(44)40-34(22-28-14-9-8-10-15-28)35(43)27-39-38(3,4)31-16-13-17-33(26-31)48-5/h8-10,13-17,23-26,34-35,39,43H,6-7,11-12,18-22,27H2,1-5H3,(H,40,44)/t34-,35+/m0/s1
InChIKeyKCQAMDDVQXZDMS-OIDHKYIRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CCCN(CCC)C(=O)c1cc(cc(c1)N2CCCCS2(=O)=O)C(=O)NC(Cc3ccccc3)C(CNC(C)(C)c4cccc(c4)OC)O
CACTVS 3.385CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CNC(C)(C)c3cccc(OC)c3)N4CCCC[S]4(=O)=O
OpenEye OEToolkits 1.9.2CCCN(CCC)C(=O)c1cc(cc(c1)N2CCCCS2(=O)=O)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CNC(C)(C)c4cccc(c4)OC)O
ACDLabs 12.01O=S4(=O)N(c3cc(C(=O)NC(Cc1ccccc1)C(O)CNC(c2cccc(OC)c2)(C)C)cc(C(=O)N(CCC)CCC)c3)CCCC4
CACTVS 3.385CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CNC(C)(C)c3cccc(OC)c3)N4CCCC[S]4(=O)=O
FormulaC38 H52 N4 O6 S
Name5-[1,1-bis(oxidanylidene)-1,2-thiazinan-2-yl]-N3-[(2S,3R)-4-[2-(3-methoxyphenyl)propan-2-ylamino]-3-oxidanyl-1-phenyl-butan-2-yl]-N1,N1-dipropyl-benzene-1,3-dicarboxamide
ChEMBLCHEMBL587764
DrugBank
ZINCZINC000049745031
PDB chain4cku Chain E Residue 400 [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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PDB4cku Plasmepsin Inhibitory Activity and Structure-Guided Optimization of a Potent Hydroxyethylamine-Based Antimalarial Hit.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		M15 I32 D34 G36 Y77 V78 S79 F111 I123 Y192 D214 G216 T217 S218 I290 L292 I300
Binding residue
(residue number reindexed from 1)		M14 I31 D33 G35 Y76 V77 S78 F110 I122 Y191 D213 G215 T216 S217 I283 L285 I293
Annotation score1
Binding affinityMOAD: ic50=0.15uM
BindingDB: IC50=150nM
Enzymatic activity
Catalytic site (original residue number in PDB) D34 S37 N39 W41 Y77 D214 T217
Catalytic site (residue number reindexed from 1) D33 S36 N38 W40 Y76 D213 T216
Enzyme Commision number 3.4.23.39: plasmepsin II.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4cku, PDBe:4cku, PDBj:4cku
PDBsum4cku
PubMed24900843
UniProtP46925|PLM2_PLAFX Plasmepsin II (Gene Name=PMII)

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