Structure of PDB 3b9g Chain A Binding Site BS02

Receptor Information

>3b9g Chain A (length=317) Species: 5699 (Trypanosoma vivax)

SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVT
GKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPE
NVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKY
GEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGC
PGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMGGGYAW
DALTAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARN
PEAEFFLDMLLRSARAC

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: 3b9g Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3b9g A Flexible Loop as a Functional Element in the Catalytic Mechanism of Nucleoside Hydrolase from Trypanosoma vivax.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): N12 D14 D40 M164 E184 N186 W250 D251
• Binding residue (residue number reindexed from 1): N12 D14 D40 M164 E184 N186 W250 D251
• Annotation score: 1
• Binding affinity: MOAD: Ki=19uM
  PDBbind-CN: -logKd/Ki=4.72,Ki=19uM

Enzymatic activity

• Catalytic site (original residue number in PDB): D10 D15 D40 W83 T137 W185 N186 W250 D251
• Catalytic site (residue number reindexed from 1): D10 D15 D40 W83 T137 W185 N186 W250 D251
• Enzyme Commision number: 3.2.2.1: purine nucleosidase.

Gene Ontology

Molecular Function

• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0046872 metal ion binding

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process

External links

• PDB: RCSB:3b9g, PDBe:3b9g, PDBj:3b9g
• PDBsum: 3b9g
• PubMed: 18519562
• UniProt: Q9GPQ4