Structure of PDB 4cku Chain F Binding Site BS01

Receptor Information
>4cku Chain F (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
VGNISLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCN
NSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFI
LGDPFMRKYFTVFDYDNHSVGIALAKKNL
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 F 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 V78 S79 F111 I123 Y192 D214 G216 T217 S218 I290 L292
Binding residue
(residue number reindexed from 1)		M15 I32 D34 G36 V78 S79 F111 I123 Y192 D214 G216 T217 S218 I290 L292
Annotation score1
Binding affinityMOAD: ic50=0.15uM
PDBbind-CN: -logKd/Ki=6.82,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) 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:4cku, PDBe:4cku, PDBj:4cku
PDBsum4cku
PubMed24900843
UniProtP46925|PLM2_PLAFX Plasmepsin II (Gene Name=PMII)

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