Structure of PDB 1nw4 Chain B Binding Site BS01

Receptor Information

>1nw4 Chain B (length=243) Species: 36329 (Plasmodium falciparum 3D7)

NLLRHLKISKEQITPVVLVVGDPGRVDKIKVVCDSYVDLAYNREYKSVEC
HYKGQKFLCVSHGVGSAGCAVCFEELCQNGAKVIIRAGSCGSLQPDLIKR
GDICICNAAVREDRVSHLLIHGDFPAVGDFDVYDTLNKCAQELNVPVFNG
ISVSSDMYYPNKIIPSRLEDYSKANAAVVEMELATLMVIGTLRKVKTGGI
LIVDGCPFKWDEGDFDNNLVPHQLENMIKIALGACAKLATKYA

Ligand information

• Ligand ID: IMH
• InChI: InChI=1S/C11H14N4O4/c16-2-5-9(17)10(18)7(15-5)4-1-12-8-6(4)13-3-14-11(8)19/h1,3,5,7,9-10,12,15-18H,2H2,(H,13,14,19)/t5-,7+,9-,10+/m1/s1
• InChIKey: IWKXDMQDITUYRK-KUBHLMPHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1c(c2c([nH]1)C(=O)NC=N2)C3C(C(C(N3)CO)O)O
  CACTVS 3.385: OC[C@H]1N[C@H]([C@H](O)[C@@H]1O)c2c[nH]c3C(=O)NC=Nc23
  ACDLabs 12.01: OC1C(NC(CO)C1O)c1c[NH]c2c1N=CNC2=O
  OpenEye OEToolkits 2.0.7: c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@@H]([C@@H]([C@H](N3)CO)O)O
  CACTVS 3.385: OC[CH]1N[CH]([CH](O)[CH]1O)c2c[nH]c3C(=O)NC=Nc23
• Formula: C11 H14 N4 O4
• Name: 1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL;
  Forodesine;
  Immucillin H
• ChEMBL: CHEMBL218291
• DrugBank: DB06185
• ZINC: ZINC000013492899
• PDB chain: 1nw4 Chain B Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1nw4 Plasmodium falciparum Purine Nucleoside Phosphorylase: CRYSTAL STRUCTURES, IMMUCILLIN INHIBITORS, AND DUAL CATALYTIC FUNCTION.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): S91 C92 G93 Y160 E182 M183 E184 D206
• Binding residue (residue number reindexed from 1): S89 C90 G91 Y158 E180 M181 E182 D204
• Annotation score: 1
• Binding affinity: MOAD: Kd=0.86nM
  PDBbind-CN: -logKd/Ki=9.07,Kd=860pM

Enzymatic activity

• Catalytic site (original residue number in PDB): H7 G23 R27 R45 E77 R88 S91 D206 G207 P209 V222
• Catalytic site (residue number reindexed from 1): H5 G21 R25 R43 E75 R86 S89 D204 G205 P207 V220
• Enzyme Commision number: 2.4.2.1: purine-nucleoside phosphorylase.
  2.4.2.44: S-methyl-5'-thioinosine phosphorylase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004731 purine-nucleoside phosphorylase activity
• GO:0004850 uridine phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0017061 S-methyl-5-thioadenosine phosphorylase activity
• GO:0047975 guanosine phosphorylase activity

Biological Process

• GO:0006148 inosine catabolic process
• GO:0006166 purine ribonucleoside salvage
• GO:0006195 purine nucleotide catabolic process
• GO:0006218 uridine catabolic process
• GO:0009116 nucleoside metabolic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:1nw4, PDBe:1nw4, PDBj:1nw4
• PDBsum: 1nw4
• PubMed: 14982926
• UniProt: Q8I3X4|PNPH_PLAF7 Purine nucleoside phosphorylase (Gene Name=PNP)