Structure of PDB 3gn2 Chain D Binding Site BS03

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 271 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		R14 F97 Y174 P210 M213
Binding residue
(residue number reindexed from 1)		R13 F96 Y155 P191 M194
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

[Back to BioLiP]