Structure of PDB 3qi3 Chain B Binding Site BS01

Receptor Information
>3qi3 Chain B (length=325) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTYPKYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRDFSI
NPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKFSQT
DILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCAVAF
QILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKEKME
NFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQSDR
EKSEGLPVAPFMDRDKVTKATAEIGFIKFVLIPMFETVTKLFPMVEEIML
QPLWESRDRYEELKRIDDAMKELQK
Ligand information
Ligand IDPDB
InChIInChI=1S/C15H12ClF3N4O/c1-8(15(17,18)19)6-12-21-13-9(14(24)22-12)7-20-23(13)11-5-3-2-4-10(11)16/h2-5,7-8H,6H2,1H3,(H,21,22,24)/t8-/m1/s1
InChIKeyFFPXPXOAFQCNBS-MRVPVSSYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01FC(F)(F)C(C)CC1=NC(=O)c2c(N1)n(nc2)c3ccccc3Cl
OpenEye OEToolkits 1.7.6CC(CC1=NC(=O)c2cnn(c2N1)c3ccccc3Cl)C(F)(F)F
CACTVS 3.385C[CH](CC1=NC(=O)c2cnn(c2N1)c3ccccc3Cl)C(F)(F)F
CACTVS 3.385
OpenEye OEToolkits 1.7.6		C[C@H](CC1=NC(=O)c2cnn(c2N1)c3ccccc3Cl)C(F)(F)F
FormulaC15 H12 Cl F3 N4 O
Name1-(2-chlorophenyl)-6-[(2R)-3,3,3-trifluoro-2-methylpropyl]-1,7-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL1513993
DrugBank
ZINCZINC000013829341
PDB chain3qi3 Chain B Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qi3 Structural asymmetry of phosphodiesterase-9, potential protonation of a glutamic Acid, and role of the invariant glutamine.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		L420 Y424 F441 A452 E453 F456
Binding residue
(residue number reindexed from 1)		L240 Y244 F261 A272 E273 F276
Annotation score1
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:3qi3, PDBe:3qi3, PDBj:3qi3
PDBsum3qi3
PubMed21483814
UniProtO76083|PDE9A_HUMAN High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (Gene Name=PDE9A)

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