Structure of PDB 3hdz Chain A Binding Site BS01

Receptor Information
>3hdz Chain A (length=323) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQ
NFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQN
KLTDLEILALLIAALSHDLDHPGVSNQFLINTNSELALMYNDESVLEHHH
FDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEF
FELIRKNQFNLEDPHEKELFLAMLMTACDLSAITKPWPIQQRIAELVATE
FFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHV
SEDCFPLLDGCRKNRQKWQALAE
Ligand information
Ligand IDPD6
InChIInChI=1S/C18H19N3O/c1-2-3-10-21-11-9-16(22)17-15(21)12-14(20-18(17)19)13-7-5-4-6-8-13/h4-9,11-12H,2-3,10H2,1H3,(H2,19,20)
InChIKeyRLCFNIHFDBMYES-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCN1C=CC(=O)c2c(N)nc(cc12)c3ccccc3
OpenEye OEToolkits 1.7.5CCCCN1C=CC(=O)c2c1cc(nc2N)c3ccccc3
FormulaC18 H19 N3 O
Name5-amino-1-butyl-7-phenyl-1,6-naphthyridin-4(1H)-one
ChEMBL
DrugBank
ZINC
PDB chain3hdz Chain A Residue 400 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3hdz Identification, synthesis and SAR of amino substituted pyrido[3,2b]pyrazinones as potent and selective PDE5 inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		A767 I768 L804 M816 Q817 F820
Binding residue
(residue number reindexed from 1)		A232 I233 L269 M281 Q282 F285
Annotation score1
Binding affinityMOAD: ic50=51nM
PDBbind-CN: -logKd/Ki=7.29,IC50=51nM
Enzymatic activity
Enzyme Commision number 3.1.4.35: 3',5'-cyclic-GMP phosphodiesterase.
3.1.4.53: 3',5'-cyclic-AMP 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

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Molecular Function
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Biological Process
External links
PDB RCSB:3hdz, PDBe:3hdz, PDBj:3hdz
PDBsum3hdz
PubMed19540112
UniProtO76074|PDE5A_HUMAN cGMP-specific 3',5'-cyclic phosphodiesterase (Gene Name=PDE5A);
P27815|PDE4A_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4A (Gene Name=PDE4A)

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