Structure of PDB 4i72 Chain A Binding Site BS02

Receptor Information
>4i72 Chain A (length=328) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMAKTVILDHDGNKDDFVAMILLLSNPKKVNLIGCICTDADCFVENGF
DVTGKIMCAMHRLIKTPLFPIGKSTATAVNAFPTEWRFSAKNLDDMPFLN
IVEDVALWEKLKPENEAHNGQQLLADLVMKSKEKVTVCVTGPLSNMAWCI
EKYGEAFTSKVEECVIMGGAVDVGGNVFLPTTDGSAEWNIYWDPPAAKKV
LCCPNIRCVLFSLDATNTVPVRSVDVKGFGAQNQYLLSQMVGTMWAMSTH
EEILRDGDAYYAWDALTAAYILEPTIATLEPVALDVDVSKGKSEGRTPRA
SGKPCVHVARNPSKQMFHDLVFASTRVC
Ligand information
Ligand IDUA2
InChIInChI=1S/C11H15N5O3/c12-11-8-6(14-3-15-11)4(1-13-8)7-10(19)9(18)5(2-17)16-7/h1,3,5,7,9-10,13,16-19H,2H2,(H2,12,14,15)/t5-,7+,9-,10+/m1/s1
InChIKeyAMFDITJFBUXZQN-KUBHLMPHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2c1[nH]cc2[C@@H]3N[C@H](CO)[C@@H](O)[C@H]3O
ACDLabs 12.01OC3C(c2c1ncnc(N)c1nc2)NC(CO)C3O
CACTVS 3.370Nc1ncnc2c1[nH]cc2[CH]3N[CH](CO)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1c(c2c([nH]1)c(ncn2)N)C3C(C(C(N3)CO)O)O
OpenEye OEToolkits 1.7.6c1c(c2c([nH]1)c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](N3)CO)O)O
FormulaC11 H15 N5 O3
Name3,4-PYRROLIDINEDIOL,2-(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)-2S,3S,4R,5R
ChEMBLCHEMBL1236524
DrugBankDB11676
ZINCZINC000013492903
PDB chain4i72 Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4i72 Structures of purine nucleosidase from Trypanosoma brucei bound to isozyme-specific trypanocidals and a novel metalorganic inhibitor
Resolution2.05 Å
Binding residue
(original residue number in PDB)		N12 D14 D40 F79 W83 M164 E184 N186 R252 Y257 W260 D261
Binding residue
(residue number reindexed from 1)		N15 D17 D43 F82 W86 M167 E187 N189 R255 Y260 W263 D264
Annotation score1
Binding affinityMOAD: Ki=0.9nM
PDBbind-CN: -logKd/Ki=9.05,Ki=0.9nM
Enzymatic activity
Enzyme Commision number 3.2.2.1: purine nucleosidase.
Gene Ontology
Molecular Function
GO:0008477 purine nucleosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
GO:0046872 metal ion binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006152 purine nucleoside catabolic process
GO:0006166 purine ribonucleoside salvage
Cellular Component
GO:0005829 cytosol
GO:0020015 glycosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4i72, PDBe:4i72, PDBj:4i72
PDBsum4i72
PubMed23897478
UniProtQ57ZL6

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