Structure of PDB 1r4f Chain B Binding Site BS02

Receptor Information
>1r4f Chain B (length=314) Species: 5699 (Trypanosoma vivax) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SAKNVVLDHDGNLDDFVAMVLLASNTEKVRLIGALCTDADCFVENGFNVT
GKIMCLMHNNMNLPLFPIGKSAATAVNPFPKEWRCLAKNMDDMPILNIPE
NVELWDKIKAENEKYEGQQLLADLVMNSEEKVTICVTGPLSNVAWCIDKY
GEKFTSKVEECVIMGGAVDVRGNVFLPSTDGTAEWNIYWDPASAKTVFGC
PGLRRIMFSLDSTNTVPVRSPYVQRFGEQTNFLLSILVGTMWAMYAADAL
TAAYVVDQKVANVDPVPIDVVVDKQPNEGATVRTDAENYPLTFVARNPEA
EFFLDMLLRSARAC
Ligand information
Ligand IDAD3
InChIInChI=1S/C11H14N4O4/c12-10-7-5(1-2-13-10)15(4-14-7)11-9(18)8(17)6(3-16)19-11/h1-2,4,6,8-9,11,16-18H,3H2,(H2,12,13)/t6-,8-,9-,11-/m1/s1
InChIKeyDBZQFUNLCALWDY-PNHWDRBUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cnc(c2c1n(cn2)C3C(C(C(O3)CO)O)O)N
CACTVS 3.341Nc1nccc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1cnc(c2c1n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
ACDLabs 10.04n1c3c(n(c1)C2OC(C(O)C2O)CO)ccnc3N
CACTVS 3.341Nc1nccc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
FormulaC11 H14 N4 O4
Name3-DEAZA-ADENOSINE
ChEMBLCHEMBL202701
DrugBankDB04546
ZINCZINC000018193375
PDB chain1r4f Chain B Residue 330 [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]
PDB1r4f Leaving group activation by aromatic stacking: an alternative to general Acid catalysis.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		N12 D14 D40 W83 M164 N173 E184 N186 D261
Binding residue
(residue number reindexed from 1)		N12 D14 D40 W83 M164 N173 E184 N186 D248
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D10 D15 D40 W83 T137 W185 N186 A260 D261
Catalytic site (residue number reindexed from 1) D10 D15 D40 W83 T137 W185 N186 A247 D248
Enzyme Commision number 3.2.2.1: purine nucleosidase.
Gene Ontology
Molecular Function
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0046872 metal ion binding
Biological Process
GO:0006139 nucleobase-containing compound metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1r4f, PDBe:1r4f, PDBj:1r4f
PDBsum1r4f
PubMed15050818
UniProtQ9GPQ4

[Back to BioLiP]