Structure of PDB 2pt9 Chain A Binding Site BS01

Receptor Information
>2pt9 Chain A (length=281) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDG
VIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSV
ENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTY
DVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTI
KNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLES
KEFADLKYYNYENHSAAFKLPAFLLKEIENI
Ligand information
Ligand IDS4M
InChIInChI=1S/C14H24N6O3S/c1-24(4-2-3-15)5-8-10(21)11(22)14(23-8)20-7-19-9-12(16)17-6-18-13(9)20/h6-8,10-11,14,21-22,24H,2-5,15H2,1H3,(H2,16,17,18)/t8-,10-,11-,14-/m1/s1
InChIKeyKIZZALRCMBIHBH-IDTAVKCVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CS(CCCN)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
OpenEye OEToolkits 1.5.0C[S@@H](CCCN)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
CACTVS 3.341C[SH](CCCN)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CS(CCCN)C)N
CACTVS 3.341C[SH](CCCN)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
FormulaC14 H24 N6 O3 S
Name5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE
ChEMBL
DrugBank
ZINC
PDB chain2pt9 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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PDB2pt9 Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Q93 H103 G124 G125 D127 E147 I148 V152 D178 A179 D196 S198 P203 A204
Binding residue
(residue number reindexed from 1)		Q53 H63 G84 G85 D87 E107 I108 V112 D138 A139 D156 S158 P163 A164
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.46,IC50=35uM
Enzymatic activity
Enzyme Commision number 2.5.1.16: spermidine synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004766 spermidine synthase activity
GO:0016740 transferase activity
Biological Process
GO:0006596 polyamine biosynthetic process
GO:0008295 spermidine biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2pt9, PDBe:2pt9, PDBj:2pt9
PDBsum2pt9
PubMed17822713
UniProtQ8II73

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