Structure of PDB 2pt9 Chain B Binding Site BS02

Receptor Information

>2pt9 Chain B (length=280) Species: 36329 (Plasmodium falciparum 3D7)

KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDG
VIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSV
ENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTY
DVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTI
KNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLES
KEFADLKYYNYENHSAAFKLPAFLLKEIEN

Ligand information

• Ligand ID: 2MH
• InChI: InChI=1S/C7H15N/c1-6-2-4-7(8)5-3-6/h6-7H,2-5,8H2,1H3/t6-,7+
• InChIKey: KSMVBYPXNKCPAJ-KNVOCYPGSA-N
• SMILES:
  CACTVS 3.341: C[C@@H]1CC[C@H](N)CC1
  CACTVS 3.341: C[CH]1CC[CH](N)CC1
  ACDLabs 10.04: NC1CCC(C)CC1
  OpenEye OEToolkits 1.5.0: CC1CCC(CC1)N
• Formula: C7 H15 N
• Name: cis-4-methylcyclohexanamine
• ZINC: ZINC000100004326
• PDB chain: 2pt9 Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2pt9 Crystal structure of Plasmodium falciparum spermidine synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): Q93 Y102 S197 D199 Y264 I269
• Binding residue (residue number reindexed from 1): Q53 Y62 S157 D159 Y224 I229
• Annotation score: 1
• Binding affinity: MOAD: 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

External links

• PDB: RCSB:2pt9, PDBe:2pt9, PDBj:2pt9
• PDBsum: 2pt9
• PubMed: 17822713
• UniProt: Q8II73