Structure of PDB 1odi Chain B Binding Site BS01

Receptor Information
>1odi Chain B (length=234) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPIHVRAHPGDVAERVLLPGDPGRAEWIAKTFLQNPRRYNDHRGLWGYTG
LYKGVPVSVQTTGMGTPSAAIVVEELVRLGARVLVRVGTAGAASSDLAPG
ELIVAQGAVPLDGTTRQYLEGRPYAPVPDPEVFRALWRRAEALGYPHRVG
LVASEDAFYATTPEEARAWARYGVLAFEMEASALFLLGRMRGVRTGAILA
VSNRIGDPELAPPEVLQEGVRRMVEVALEAVLEV
Ligand information
Ligand IDADN
InChIInChI=1S/C10H13N5O4/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(18)6(17)4(1-16)19-10/h2-4,6-7,10,16-18H,1H2,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1
InChIKeyOIRDTQYFTABQOQ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O)[CH]3O
ACDLabs 10.04n2c1c(ncnc1n(c2)C3OC(C(O)C3O)CO)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)O)O)N
FormulaC10 H13 N5 O4
NameADENOSINE
ChEMBLCHEMBL477
DrugBankDB00640
ZINCZINC000002169830
PDB chain1odi Chain A Residue 1237 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1odi Crystal Structure of Purine Nucleoside Phosphorylase from Thermus Thermophilus
Resolution2.4 Å
Binding residue
(original residue number in PDB)		H5 R44
Binding residue
(residue number reindexed from 1)		H4 R43
Annotation score3
Binding affinityMOAD: Kd=62uM
PDBbind-CN: -logKd/Ki=4.21,Kd=62uM
Enzymatic activity
Catalytic site (original residue number in PDB) H5 G21 R25 R44 E76 R87 T90 S203 N204 I206 L217
Catalytic site (residue number reindexed from 1) H4 G20 R24 R43 E75 R86 T89 S202 N203 I205 L216
Enzyme Commision number 2.4.2.3: uridine phosphorylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
Biological 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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Biological Process
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Cellular Component
External links
PDB RCSB:1odi, PDBe:1odi, PDBj:1odi
PDBsum1odi
PubMed15046984
UniProtQ5SID9

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