Structure of PDB 6f4w Chain E Binding Site BS02

Receptor Information
>6f4w Chain E (length=233) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTPHINAKIGDFYPQCLLCGDPLRVSYIAKKFLQDAKEITNVRNMLGFSG
KYKGRGISLMGHGMGIASCTIYVTELIKTYQVKELLRIGTCGAISPKVGL
KDIIMATGASTDSKTNRVRFLNHDLSATPDFELSLRAYQTAKRLGIDLKV
GNVFSSDFFYSFETHAFDLMAKYNHLAIEMEAAGLYATAMELNAKALCLC
SVSDHLITKEALSPKERVESFDNMIILALEMMS
Ligand information
Ligand IDFMC
InChIInChI=1S/C10H13N5O4/c11-10-6-4(12-2-13-10)5(14-15-6)9-8(18)7(17)3(1-16)19-9/h2-3,7-9,16-18H,1H2,(H,14,15)(H2,11,12,13)/t3-,7-,8-,9+/m1/s1
InChIKeyKBHMEHLJSZMEMI-KSYZLYKTSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2c1[nH]nc2[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2c1[nH]nc2[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 12.01OC1C(OC(CO)C1O)c3nnc2c3ncnc2N
OpenEye OEToolkits 1.7.0c1nc2c(c(n1)N)[nH]nc2C3C(C(C(O3)CO)O)O
OpenEye OEToolkits 1.7.0c1nc2c(c(n1)N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
FormulaC10 H13 N5 O4
Name(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol
ChEMBLCHEMBL471524
DrugBankDB02281
ZINCZINC000018275505
PDB chain6f4w Chain E Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6f4w Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
Resolution2.293 Å
Binding residue
(original residue number in PDB)		T90 C91 G92 F159 M180 E181
Binding residue
(residue number reindexed from 1)		T90 C91 G92 F159 M180 E181
Annotation score1
Binding affinityMOAD: Kd=2.95uM
Enzymatic activity
Catalytic site (original residue number in PDB) H4 G20 R24 R43 E75 R87 T90 S203 D204 L206 R217
Catalytic site (residue number reindexed from 1) H4 G20 R24 R43 E75 R87 T90 S203 D204 L206 R217
Enzyme Commision number 2.4.2.1: purine-nucleoside phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004731 purine-nucleoside phosphorylase activity
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006152 purine nucleoside catabolic process
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Cellular Component
External links
PDB RCSB:6f4w, PDBe:6f4w, PDBj:6f4w
PDBsum6f4w
PubMed29430816
UniProtP56463|DEOD_HELPY Purine nucleoside phosphorylase DeoD-type (Gene Name=deoD)

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