Structure of PDB 3fnu Chain A Binding Site BS01

Receptor Information

>3fnu Chain A (length=326) Species: 36329 (Plasmodium falciparum 3D7)

EFDNVELKDLANVLSFGEAKLGDNGQKFNFLFHTASSNVWVPSIKCTSES
CESKNHYDSSKSKTYEKDDTPVKLTSKAGTISGIFSKDLVTIGKLSVPYK
FIEMTEIVGFEPFYSESDVDGVFGLGWKDLSIGSIDPYIVELKTQNKIEQ
AVYSIYLPPENKNKGYLTIGGIEERFFDGPLNYEKLNHDLMWQVDLDVHF
GNVSSKKANVILDSATSVITVPTEFFNQFVESASVFKVPFLSLYVTTCGN
TKLPTLEYRSPNKVYTLEPKQYLEPLENIFSALCMLNIVPIDLEKNTFVL
GDPFMRKYFTVYDYDNHTVGFALAKN

Ligand information

• Ligand ID: 006
• InChI: InChI=1S/C35H41N3O6S/c1-21-11-10-12-22(2)31(21)44-19-28(40)36-26(17-23-13-6-5-7-14-23)30(41)34(43)38-20-45-35(3,4)32(38)33(42)37-29-25-16-9-8-15-24(25)18-27(29)39/h5-16,26-27,29-30,32,39,41H,17-20H2,1-4H3,(H,36,40)(H,37,42)/t26-,27+,29-,30-,32+/m0/s1
• InChIKey: KKTYZYHUPKXLPL-RIQJEONASA-N
• SMILES:
  CACTVS 3.370: Cc1cccc(C)c1OCC(=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
  ACDLabs 12.01: O=C(NC2c1ccccc1CC2O)C5N(C(=O)C(O)C(NC(=O)COc3c(cccc3C)C)Cc4ccccc4)CSC5(C)C
  CACTVS 3.370: Cc1cccc(C)c1OCC(=O)N[CH](Cc2ccccc2)[CH](O)C(=O)N3CSC(C)(C)[CH]3C(=O)N[CH]4[CH](O)Cc5ccccc45
  OpenEye OEToolkits 1.7.0: Cc1cccc(c1OCC(=O)NC(Cc2ccccc2)C(C(=O)N3CSC(C3C(=O)NC4c5ccccc5CC4O)(C)C)O)C
  OpenEye OEToolkits 1.7.0: Cc1cccc(c1OCC(=O)N[C@@H](Cc2ccccc2)[C@@H](C(=O)N3CSC([C@H]3C(=O)N[C@H]4c5ccccc5C[C@H]4O)(C)C)O)C
• Formula: C35 H41 N3 O6 S
• Name: (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide;
  KNI-10006
• ChEMBL: CHEMBL231522
• ZINC: ZINC000028703797
• PDB chain: 3fnu Chain A Residue 329

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3fnu Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): W39 F109A F111 Y112 V120
• Binding residue (residue number reindexed from 1): W40 F110 F113 Y114 V122
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.16,IC50=0.69uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H32 S35 N37 W39 S75 D215 T218
• Catalytic site (residue number reindexed from 1): H33 S36 N38 W40 S76 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

External links

• PDB: RCSB:3fnu, PDBe:3fnu, PDBj:3fnu
• PDBsum: 3fnu
• PubMed: 19285084
• UniProt: Q8IM15|PLM3_PLAF7 Plasmepsin III (Gene Name=PMIII)