Structure of PDB 2wd8 Chain D Binding Site BS02

Receptor Information

>2wd8 Chain D (length=249) Species: 5702 (Trypanosoma brucei brucei)

EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKE
RSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTP
LVGKTVETQVAELIGTNAIAPFLLTMSFAQRQSNLSIVNLCDAMVDQPCM
AFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKD
KWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA

Ligand information

• Ligand ID: VGF
• InChI: InChI=1S/C20H15Cl2N3/c21-16-10-9-13(11-17(16)22)12-25-19-15(14-5-2-1-3-6-14)7-4-8-18(19)24-20(25)23/h1-11H,12H2,(H2,23,24)
• InChIKey: JFVMZMBFRZPOFF-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.352: Nc1nc2cccc(c3ccccc3)c2n1Cc4ccc(Cl)c(Cl)c4
  OpenEye OEToolkits 1.6.1: c1ccc(cc1)c2cccc3c2n(c(n3)N)Cc4ccc(c(c4)Cl)Cl
  ACDLabs 10.04: Clc1ccc(cc1Cl)Cn2c3c(nc2N)cccc3c4ccccc4
• Formula: C20 H15 Cl2 N3
• Name: 1-(3,4-DICHLOROBENZYL)-7-PHENYL-1H-BENZIMIDAZOL-2-AMINE
• ChEMBL: CHEMBL484995
• ZINC: ZINC000040943275
• PDB chain: 2wd8 Chain D Residue 1269

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2wd8 One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): F97 D161 M163 C168 F171 G205 V206 W221 L263
• Binding residue (residue number reindexed from 1): F96 D142 M144 C149 F152 G186 V187 W202 L244
• Annotation score: 1
• Binding affinity: MOAD: Kd=10.6uM
  BindingDB: Ki=7nM

Enzymatic activity

• Catalytic site (original residue number in PDB): R14 D161 Y174 K178
• Catalytic site (residue number reindexed from 1): R13 D142 Y155 K159
• Enzyme Commision number: 1.5.1.33: pteridine reductase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0047040 pteridine reductase activity

External links

• PDB: RCSB:2wd8, PDBe:2wd8, PDBj:2wd8
• PDBsum: 2wd8
• PubMed: 19527033
• UniProt: O76290