Structure of PDB 3shy Chain A Binding Site BS01

Receptor Information
>3shy Chain A (length=298) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLV
QNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQ
NKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHSIMEHHHFDQCLMIL
NSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQ
FNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQKKNK
IPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
Ligand information
Ligand ID5FO
InChIInChI=1S/C20H27FN4O4S/c1-4-12-29-17-7-6-14(30(27,28)25-10-8-24(3)9-11-25)13-15(17)19-22-16(5-2)18(21)20(26)23-19/h6-7,13H,4-5,8-12H2,1-3H3,(H,22,23,26)
InChIKeyMMOIQVJIHPNAIU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=S(=O)(c2cc(C1=NC(=C(F)C(=O)N1)CC)c(OCCC)cc2)N3CCN(C)CC3
OpenEye OEToolkits 1.7.2CCCOc1ccc(cc1C2=NC(=C(C(=O)N2)F)CC)S(=O)(=O)N3CCN(CC3)C
CACTVS 3.370CCCOc1ccc(cc1C2=NC(=C(F)C(=O)N2)CC)[S](=O)(=O)N3CCN(C)CC3
FormulaC20 H27 F N4 O4 S
Name6-ethyl-5-fluoro-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one
ChEMBLCHEMBL1915517
DrugBank
ZINCZINC000073159181
PDB chain3shy Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3shy Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors.
Resolution2.647 Å
Binding residue
(original residue number in PDB)		V782 F786 M816 Q817 F820
Binding residue
(residue number reindexed from 1)		V239 F243 M254 Q255 F258
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.04,IC50=90.9nM
BindingDB: Kd=1700nM
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
Gene Ontology
Molecular Function
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0007165 signal transduction

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3shy, PDBe:3shy, PDBj:3shy
PDBsum3shy
PubMed21714539
UniProtO76074|PDE5A_HUMAN cGMP-specific 3',5'-cyclic phosphodiesterase (Gene Name=PDE5A)

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