Structure of PDB 3gn2 Chain D Binding Site BS02

Receptor Information
>3gn2 Chain D (length=249) Species: 5702 (Trypanosoma brucei brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKE
RSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTP
LVGKTVETQVAELIGTNAIAPFLLTMSFAQRQSNLSIVNLCDAMVDQPCM
AFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKD
KWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA
Ligand information
Ligand IDAX8
InChIInChI=1S/C14H11Cl2N3/c15-10-6-5-9(7-11(10)16)8-19-13-4-2-1-3-12(13)18-14(19)17/h1-7H,8H2,(H2,17,18)
InChIKeyJBNABAJVIVYIDA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc1ccc(cc1Cl)Cn2c3ccccc3nc2N
CACTVS 3.341Nc1nc2ccccc2n1Cc3ccc(Cl)c(Cl)c3
OpenEye OEToolkits 1.5.0c1ccc2c(c1)nc(n2Cc3ccc(c(c3)Cl)Cl)N
FormulaC14 H11 Cl2 N3
Name1-(3,4-dichlorobenzyl)-1H-benzimidazol-2-amine
ChEMBLCHEMBL520667
DrugBank
ZINCZINC000000461252
PDB chain3gn2 Chain D Residue 270 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3gn2 One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		F97 D161 M163 C168 F171 G205 W221 L263
Binding residue
(residue number reindexed from 1)		F96 D142 M144 C149 F152 G186 W202 L244
Annotation score1
Binding affinityMOAD: Ki=0.4uM
BindingDB: Ki=400nM
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 ?
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016491 oxidoreductase activity
GO:0047040 pteridine reductase activity

View graph for
Molecular Function
External links
PDB RCSB:3gn2, PDBe:3gn2, PDBj:3gn2
PDBsum3gn2
PubMed19527033
UniProtO76290

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