Structure of PDB 1pf7 Chain E Binding Site BS01

Receptor Information
>1pf7 Chain E (length=288) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYS
EIPNFPRSTVPGHAGRLVFGFLNGRACVMMQGRFHMYEGYPLWKVTFPVR
VFHLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLPGFSGQNPLRGPN
DERFGDRFPAMSDAYDRTMRQRALSTWKQMGEQRELQEGTYVMVAGPSFE
TVAECRVLQKLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYES
LEKANHEEVLAAGKQAAQKLEQFVSILMASIPLPDKAS
Ligand information
Ligand IDIMH
InChIInChI=1S/C11H14N4O4/c16-2-5-9(17)10(18)7(15-5)4-1-12-8-6(4)13-3-14-11(8)19/h1,3,5,7,9-10,12,15-18H,2H2,(H,13,14,19)/t5-,7+,9-,10+/m1/s1
InChIKeyIWKXDMQDITUYRK-KUBHLMPHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1c(c2c([nH]1)C(=O)NC=N2)C3C(C(C(N3)CO)O)O
CACTVS 3.385OC[C@H]1N[C@H]([C@H](O)[C@@H]1O)c2c[nH]c3C(=O)NC=Nc23
ACDLabs 12.01OC1C(NC(CO)C1O)c1c[NH]c2c1N=CNC2=O
OpenEye OEToolkits 2.0.7c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@@H]([C@@H]([C@H](N3)CO)O)O
CACTVS 3.385OC[CH]1N[CH]([CH](O)[CH]1O)c2c[nH]c3C(=O)NC=Nc23
FormulaC11 H14 N4 O4
Name1,4-DIDEOXY-4-AZA-1-(S)-(9-DEAZAHYPOXANTHIN-9-YL)-D-RIBITOL;
Forodesine;
Immucillin H
ChEMBLCHEMBL218291
DrugBankDB06185
ZINCZINC000013492899
PDB chain1pf7 Chain E Residue 290 [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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PDB1pf7 Structural basis for inhibition of human PNP by immucillin-H
Resolution2.6 Å
Binding residue
(original residue number in PDB)		Y88 A116 E201 M219 T242 N243 H257
Binding residue
(residue number reindexed from 1)		Y87 A115 E200 M218 T241 N242 H256
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.14,Ki=72pM
Enzymatic activity
Catalytic site (original residue number in PDB) S33 H64 H86 Y88 E89 A116 M219 S220 N243 H257
Catalytic site (residue number reindexed from 1) S32 H63 H85 Y87 E88 A115 M218 S219 N242 H256
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:1pf7, PDBe:1pf7, PDBj:1pf7
PDBsum1pf7
PubMed13679061
UniProtP00491|PNPH_HUMAN Purine nucleoside phosphorylase (Gene Name=PNP)

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