Structure of PDB 3k8o Chain E Binding Site BS01

Receptor Information
>3k8o Chain E (length=283) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYSE
IPNFPRSTVPGHAGRLVFGFLNGRACVMMQGRFHMYEGYPLWKVTFPVRV
FHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLPGFSGQNPLRGPND
ERFGDRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMVAGPSFET
VAECRVLQKLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESL
EKANHEEVLAAGKQAAQKLEQFVSILMASIPLP
Ligand information
Ligand ID229
InChIInChI=1S/C11H16N4O4/c16-3-7(8(18)4-17)12-1-6-2-13-10-9(6)14-5-15-11(10)19/h2,5,7-8,12-13,16-18H,1,3-4H2,(H,14,15,19)/t7-,8-/m1/s1
InChIKeyCGYSFECPLYEOMH-HTQZYQBOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1c(c2c([nH]1)C(=O)NC=N2)CN[C@H](CO)[C@@H](CO)O
CACTVS 3.341OC[CH](O)[CH](CO)NCc1c[nH]c2C(=O)NC=Nc12
OpenEye OEToolkits 1.5.0c1c(c2c([nH]1)C(=O)NC=N2)CNC(CO)C(CO)O
ACDLabs 10.04O=C1c2c(N=CN1)c(cn2)CNC(C(O)CO)CO
CACTVS 3.341OC[C@@H](O)[C@@H](CO)NCc1c[nH]c2C(=O)NC=Nc12
FormulaC11 H16 N4 O4
Name7-({[(1R,2S)-2,3-DIHYDROXY-1-(HYDROXYMETHYL)PROPYL]AMINO}METHYL)-3,5-DIHYDRO-4H-PYRROLO[3,2-D]PYRIMIDIN-4-ONE
ChEMBLCHEMBL475537
DrugBank
ZINCZINC000096900972
PDB chain3k8o Chain E Residue 9006 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3k8o Crystal structure of human purine nucleoside phosphorylase in complex with DATMe-Immucillin H
Resolution2.4 Å
Binding residue
(original residue number in PDB)		A116 A117 G118 F200 E201 G218 M219 N243 H257
Binding residue
(residue number reindexed from 1)		A114 A115 G116 F198 E199 G216 M217 N241 H255
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=11.07,Kd=8.6pM
BindingDB: Ki=780nM,Kd=0.0086nM
Enzymatic activity
Catalytic site (original residue number in PDB) S33 H64 H86 Y88 E89 A116 M219 S220 N243 V245 H257
Catalytic site (residue number reindexed from 1) S31 H62 H84 Y86 E87 A114 M217 S218 N241 V243 H255
Enzyme Commision number 2.4.2.1: purine-nucleoside phosphorylase.
Gene Ontology
Molecular Function
GO:0001882 nucleoside binding
GO:0002060 purine nucleobase binding
GO:0003824 catalytic activity
GO:0004731 purine-nucleoside phosphorylase activity
GO:0005515 protein binding
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
GO:0042301 phosphate ion binding
GO:0042802 identical protein binding
GO:0047975 guanosine phosphorylase activity
Biological Process
GO:0000255 allantoin metabolic process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006148 inosine catabolic process
GO:0006149 deoxyinosine catabolic process
GO:0006157 deoxyadenosine catabolic process
GO:0006166 purine ribonucleoside salvage
GO:0006204 IMP catabolic process
GO:0006738 nicotinamide riboside catabolic process
GO:0006955 immune response
GO:0009116 nucleoside metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0009410 response to xenobiotic stimulus
GO:0032743 positive regulation of interleukin-2 production
GO:0034418 urate biosynthetic process
GO:0042102 positive regulation of T cell proliferation
GO:0043101 purine-containing compound salvage
GO:0046059 dAMP catabolic process
GO:0046638 positive regulation of alpha-beta T cell differentiation
Cellular Component
GO:0005576 extracellular region
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0034774 secretory granule lumen
GO:0070062 extracellular exosome
GO:1904813 ficolin-1-rich granule lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3k8o, PDBe:3k8o, PDBj:3k8o
PDBsum3k8o
PubMed
UniProtP00491|PNPH_HUMAN Purine nucleoside phosphorylase (Gene Name=PNP)

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