Structure of PDB 4y8c Chain A Binding Site BS01

Receptor Information
>4y8c Chain A (length=322) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSINPVT
LRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQTDILI
LMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAFQILA
EPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKMENFDY
SNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDREKSE
GLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEEIMLQPLW
ESRDRYEELKRIDDAMKELQKK
Ligand information
Ligand ID49D
InChIInChI=1S/C18H20ClN5O/c1-11(12-6-8-13(19)9-7-12)21-18-22-16-15(17(25)23-18)10-20-24(16)14-4-2-3-5-14/h6-11,14H,2-5H2,1H3,(H2,21,22,23,25)/t11-/m0/s1
InChIKeyFIUCLBJMUGCQTF-NSHDSACASA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc1ccc(cc1)C(NC2=Nc3c(C(=O)N2)cnn3C4CCCC4)C
CACTVS 3.385C[C@H](NC1=Nc2n(ncc2C(=O)N1)C3CCCC3)c4ccc(Cl)cc4
OpenEye OEToolkits 1.9.2CC(c1ccc(cc1)Cl)NC2=Nc3c(cnn3C4CCCC4)C(=O)N2
CACTVS 3.385C[CH](NC1=Nc2n(ncc2C(=O)N1)C3CCCC3)c4ccc(Cl)cc4
OpenEye OEToolkits 1.9.2C[C@@H](c1ccc(cc1)Cl)NC2=Nc3c(cnn3C4CCCC4)C(=O)N2
FormulaC18 H20 Cl N5 O
Name6-{[(1S)-1-(4-chlorophenyl)ethyl]amino}-1-cyclopentyl-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL5285855
DrugBank
ZINCZINC000263620419
PDB chain4y8c Chain A Residue 601 [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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PDB4y8c Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		M365 L420 L421 Y424 M442 A452 Q453 F456
Binding residue
(residue number reindexed from 1)		M181 L236 L237 Y240 M258 A268 Q269 F272
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.96,IC50=11nM
BindingDB: IC50=6.00nM
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:0004115 3',5'-cyclic-AMP phosphodiesterase activity
GO:0004117 calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity
GO:0005515 protein binding
GO:0008081 phosphoric diester hydrolase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity
GO:0048101 calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity
Biological Process
GO:0007165 signal transduction
GO:0010613 positive regulation of cardiac muscle hypertrophy
GO:0019933 cAMP-mediated signaling
GO:0046068 cGMP metabolic process
GO:0046069 cGMP catabolic process
GO:1900273 positive regulation of long-term synaptic potentiation
GO:2000178 negative regulation of neural precursor cell proliferation
Cellular Component
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0032587 ruffle membrane
GO:0042383 sarcolemma
GO:0042995 cell projection
GO:0043204 perikaryon
GO:0048471 perinuclear region of cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4y8c, PDBe:4y8c, PDBj:4y8c
PDBsum4y8c
PubMed26316540
UniProtO76083|PDE9A_HUMAN High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (Gene Name=PDE9A)

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