Structure of PDB 4cxm Chain A Binding Site BS01

Receptor Information

>4cxm Chain A (length=281) Species: 36329 (Plasmodium falciparum 3D7)

KKWFSEFSIMWPGQAFSLKIKKILYETKSKYQNVLVFESTTYGKVLVLDG
VIQLTEKDEFAYHEMMTHVPMTVSKEPKNVLVVGGGDGGIIRELCKYKSV
ENIDICEIDETVIEVSKIYFKNISCGYEDKRVNVFIEDASKFLENVTNTY
DVIIVDSSDPIGPAETLFNQNFYEKIYNALKPNGYCVAQCESLWIHVGTI
KNMIGYAKKLFKKVEYANISIPTYPCGCIGILCCSKTDTGLTKPNKKLES
KEFADLKYYNYENHSAAFKLPAFLLKEIENI

Ligand information

• Ligand ID: MTA
• InChI: InChI=1S/C11H15N5O3S/c1-20-2-5-7(17)8(18)11(19-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H2,12,13,14)/t5-,7-,8-,11-/m1/s1
• InChIKey: WUUGFSXJNOTRMR-IOSLPCCCSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CSCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  ACDLabs 10.04: n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CSC)N
  CACTVS 3.341: CSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
• Formula: C11 H15 N5 O3 S
• Name: 5'-DEOXY-5'-METHYLTHIOADENOSINE
• ChEMBL: CHEMBL277041
• DrugBank: DB02282
• ZINC: ZINC000004228245
• PDB chain: 4cxm Chain A Residue 540

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4cxm Three-Dimensional Structures of Plasmodium Falciparum Spermidine Synthase with Bound Inhibitors Suggest New Strategies for Drug Design.
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): G124 G125 D127 E147 I148 V152 D178 A179 D196 S198 P203 A204
• Binding residue (residue number reindexed from 1): G84 G85 D87 E107 I108 V112 D138 A139 D156 S158 P163 A164
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.5.1.16: spermidine synthase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity

External links

• PDB: RCSB:4cxm, PDBe:4cxm, PDBj:4cxm
• PDBsum: 4cxm
• PubMed: 25760598
• UniProt: Q8II73