Structure of PDB 4e90 Chain A Binding Site BS02

Receptor Information
>4e90 Chain A (length=328) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMTYPKYLLSPETIEALRKPTFDVWLWEPNEMLSCLEHMYHDLGLVRD
FSINPVTLRRWLFCVHDNYRNNPFHNFRHCFCVAQMMYSMVWLCSLQEKF
SQTDILILMTAAICHDLDHPGYNNTYQINARTELAVRYNDISPLENHHCA
VAFQILAEPECNIFSNIPPDGFKQIRQGMITLILATDMARHAEIMDSFKE
KMENFDYSNEEHMTLLKMILIKCCDISNEVRPMEVAEPWVDCLLEEYFMQ
SDREKSEGLPVAPFMDRDKVTKATAQIGFIKFVLIPMFETVTKLFPMVEE
IMLQPLWESRDRYEELKRIDDAMKELQK
Ligand information
Ligand ID7RG
InChIInChI=1S/C20H25N7O2/c1-13-10-26(12-17-21-5-2-6-22-17)11-16(13)18-24-19-15(20(28)25-18)9-23-27(19)14-3-7-29-8-4-14/h2,5-6,9,13-14,16H,3-4,7-8,10-12H2,1H3,(H,24,25,28)/t13-,16-/m1/s1
InChIKeyIWXUVYOOUMLUTQ-CZUORRHYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370C[C@@H]1CN(C[C@H]1C2=Nc3n(ncc3C(=O)N2)C4CCOCC4)Cc5ncccn5
CACTVS 3.370C[CH]1CN(C[CH]1C2=Nc3n(ncc3C(=O)N2)C4CCOCC4)Cc5ncccn5
OpenEye OEToolkits 1.7.6CC1CN(CC1C2=Nc3c(cnn3C4CCOCC4)C(=O)N2)Cc5ncccn5
OpenEye OEToolkits 1.7.6C[C@@H]1C[N@@](C[C@H]1C2=Nc3c(cnn3C4CCOCC4)C(=O)N2)Cc5ncccn5
ACDLabs 12.01O=C2NC(=Nc1n(ncc12)C3CCOCC3)C5C(C)CN(Cc4ncccn4)C5
FormulaC20 H25 N7 O2
Name6-[(3S,4S)-4-methyl-1-(pyrimidin-2-ylmethyl)pyrrolidin-3-yl]-1-(tetrahydro-2H-pyran-4-yl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL2179105
DrugBankDB11953
ZINCZINC000068199983
PDB chain4e90 Chain A Residue 903 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4e90 Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L420 Y424 F441 Q453 F456
Binding residue
(residue number reindexed from 1)		L243 Y247 F264 Q276 F279
Annotation score1
Binding affinityMOAD: ic50=8nM
PDBbind-CN: -logKd/Ki=8.10,IC50=8nM
BindingDB: IC50=70.0nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4e90, PDBe:4e90, PDBj:4e90
PDBsum4e90
PubMed23025719
UniProtO76083|PDE9A_HUMAN High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (Gene Name=PDE9A)

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