Structure of PDB 2wd7 Chain A Binding Site BS02

Receptor Information

>2wd7 Chain A (length=249) Species: 5702 (Trypanosoma brucei brucei)

EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKE
RSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTP
LVGKTVETQVAELIGTNAIAPFLLTMSFAQRQSNLSIVNLCDAMVDQPCM
AFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKD
KWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA

Ligand information

• Ligand ID: VGD
• InChI: InChI=1S/C7H6ClN3/c8-4-1-2-5-6(3-4)11-7(9)10-5/h1-3H,(H3,9,10,11)
• InChIKey: PDOCNPCPPLPXRV-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: Clc2cc1c(nc(n1)N)cc2
  CACTVS 3.341: Nc1[nH]c2cc(Cl)ccc2n1
  OpenEye OEToolkits 1.5.0: c1cc2c(cc1Cl)[nH]c(n2)N
• Formula: C7 H6 Cl N3
• Name: 6-chloro-1H-benzimidazol-2-amine
• ChEMBL: CHEMBL269158
• ZINC: ZINC000005425419
• PDB chain: 2wd7 Chain A Residue 1269

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2wd7 One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): S95 F97 Y174
• Binding residue (residue number reindexed from 1): S94 F96 Y155
• Annotation score: 1
• Binding affinity: MOAD: Ki=10.6uM
  PDBbind-CN: -logKd/Ki=4.97,Ki=10.6uM
  BindingDB: Ki=10600nM

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:2wd7, PDBe:2wd7, PDBj:2wd7
• PDBsum: 2wd7
• PubMed: 19527033
• UniProt: O76290