Structure of PDB 1lee Chain A Binding Site BS01

Receptor Information

>1lee Chain A (length=331) Species: 5833 (Plasmodium falciparum)

LGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCT
TAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSL
PYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNK
IENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLD
AHVGNISLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTL
CNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPT
FILGDPFMRKYFTVFDYDNHSVGIALAKKNL

Ligand information

• Ligand ID: R36
• InChI: InChI=1S/C32H41N3O4/c1-21(2)16-27(34-32(38)25-14-9-15-26(33)18-25)19-29(36)28(17-24-12-6-5-7-13-24)35-30(37)20-39-31-22(3)10-8-11-23(31)4/h5-15,18,21,27-29,36H,16-17,19-20,33H2,1-4H3,(H,34,38)(H,35,37)/t27-,28-,29-/m0/s1
• InChIKey: WQUBEIMCFHCJCO-AWCRTANDSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@H](C[C@H](CC(C)C)NC(=O)c3cccc(c3)N)O)C
  CACTVS 3.341: CC(C)C[C@@H](C[C@H](O)[C@H](Cc1ccccc1)NC(=O)COc2c(C)cccc2C)NC(=O)c3cccc(N)c3
  ACDLabs 10.04: O=C(c1cccc(N)c1)NC(CC(C)C)CC(O)C(NC(=O)COc2c(cccc2C)C)Cc3ccccc3
  OpenEye OEToolkits 1.5.0: Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(CC(CC(C)C)NC(=O)c3cccc(c3)N)O)C
  CACTVS 3.341: CC(C)C[CH](C[CH](O)[CH](Cc1ccccc1)NC(=O)COc2c(C)cccc2C)NC(=O)c3cccc(N)c3
• Formula: C32 H41 N3 O4
• Name: 4-AMINO-N-{4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-1-ISOBUTYL-5-PHENYL-PENTYL}-BENZAMIDE
• DrugBank: DB04373
• ZINC: ZINC000015658067
• PDB chain: 1lee Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1lee Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 A in complex with the inhibitors rs367 and rs370.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): D34 G36 N76 Y77 V78 S79 F111 I123 L131 Y192 D214 G216 T217 I290 I300
• Binding residue (residue number reindexed from 1): D36 G38 N78 Y79 V80 S81 F113 I125 L133 Y194 D216 G218 T219 I292 I302
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.74,Ki=18nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D34 S37 N39 W41 Y77 D214 T217
• Catalytic site (residue number reindexed from 1): D36 S39 N41 W43 Y79 D216 T219
• Enzyme Commision number: 3.4.23.39: plasmepsin II.

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:1lee, PDBe:1lee, PDBj:1lee
• PDBsum: 1lee
• PubMed: 12454457
• UniProt: P46925|PLM2_PLAFX Plasmepsin II (Gene Name=PMII)