Structure of PDB 5b25 Chain B Binding Site BS02

Receptor Information
>5b25 Chain B (length=332) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TYSTAVLNCLKNLDLWCFDVFSLNQAADDHALRTIVFELLTRHNLISRFK
IPTVFLMSFLDALETGYGKYKNPYHNQIHAADVTQTVHCFLLRTGMVHCL
SEIELLAIIFAAAIHDYEHTGTTNSFHIQTKSECAIVYNDRSVLENHHIS
SVFRLMQDDEMNIFINLTKDEFVELRALVIEMVLATDMSCHFQQVKTMKT
ALQQLERIDKPKALSLLLHAADISHPTKQWLVHSRWTKALMEEFFRQGDK
EAELGLPFSPLCDRTSTLVAQSQIGFIDFIVEPTFSVLTDVAEKSVQPLA
GDPNPDVVSFRSTWVKRIQENKQKWKERAASG
Ligand information
Ligand ID4QJ
InChIInChI=1S/C29H26FN7O/c1-35-28(38)25-26(31-20-7-3-2-4-8-20)36(34-27(25)37-23-11-5-10-22(23)33-29(35)37)17-18-13-15-19(16-14-18)21-9-6-12-24(30)32-21/h2-4,6-9,12-16,22-23,31H,5,10-11,17H2,1H3/t22-,23+/m1/s1
InChIKeyBBIPVJCGIASXJB-PKTZIBPZSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=O)c2c(Nc3ccccc3)n(Cc4ccc(cc4)c5cccc(F)n5)nc2N6[CH]7CCC[CH]7N=C16
OpenEye OEToolkits 2.0.4CN1C(=O)c2c(nn(c2Nc3ccccc3)Cc4ccc(cc4)c5cccc(n5)F)N6C1=N[C@H]7[C@@H]6CCC7
OpenEye OEToolkits 2.0.4CN1C(=O)c2c(nn(c2Nc3ccccc3)Cc4ccc(cc4)c5cccc(n5)F)N6C1=NC7C6CCC7
CACTVS 3.385CN1C(=O)c2c(Nc3ccccc3)n(Cc4ccc(cc4)c5cccc(F)n5)nc2N6[C@H]7CCC[C@H]7N=C16
FormulaC29 H26 F N7 O
Name(11R,15S)-4-{[4-(6-fluoropyridin-2-yl)phenyl]methyl}-8-methyl-5-(phenylamino)-1,3,4,8,10-pentaazatetracyclo[7.6.0.02,6.011,15]pentadeca-2,5,9-trien-7-one
ChEMBLCHEMBL3769414
DrugBankDB15039
ZINCZINC000142626599
PDB chain5b25 Chain B Residue 603 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5b25 Discovery of Potent and Selective Inhibitors of Phosphodiesterase 1 for the Treatment of Cognitive Impairment Associated with Neurodegenerative and Neuropsychiatric Diseases
Resolution1.9 Å
Binding residue
(original residue number in PDB)		I371 H373 L388 F392 L409 S420 Q421 G423 F424 F427
Binding residue
(residue number reindexed from 1)		I223 H225 L240 F244 L261 S272 Q273 G275 F276 F279
Annotation score1
Binding affinityMOAD: Ki=0.058nM
BindingDB: IC50=0.058000nM
Enzymatic activity
Enzyme Commision number 3.1.4.17: 3',5'-cyclic-nucleotide 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:5b25, PDBe:5b25, PDBj:5b25
PDBsum5b25
PubMed26789933
UniProtQ01064|PDE1B_HUMAN Dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B (Gene Name=PDE1B)

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