Structure of PDB 3dyl Chain A Binding Site BS02

Receptor Information
>3dyl 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 IDPCG
InChIInChI=1S/C10H12N5O7P/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6-3(21-9)1-20-23(18,19)22-6/h2-3,5-6,9,16H,1H2,(H,18,19)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyZOOGRGPOEVQQDX-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C4C(O3)COP(=O)(O4)O)O)N=C(NC2=O)N
ACDLabs 10.04O=C4NC(=Nc1c4ncn1C3OC2COP(=O)(OC2C3O)O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@H]4C(O3)CO[P@](=O)(O4)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@@H]4CO[P@](O)(=O)O[C@H]4[C@H]3O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH]4CO[P](O)(=O)O[CH]4[CH]3O
FormulaC10 H12 N5 O7 P
NameCYCLIC GUANOSINE MONOPHOSPHATE
ChEMBLCHEMBL395336
DrugBankDB02315
ZINCZINC000004095501
PDB chain3dyl Chain A Residue 900 [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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PDB3dyl Structural basis for the catalytic mechanism of human phosphodiesterase 9.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		H252 D293 M365 D402 I403 L420 Y424 Q453 F456
Binding residue
(residue number reindexed from 1)		H75 D116 M188 D225 I226 L243 Y247 Q276 F279
Annotation score4
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dyl, PDBe:3dyl, PDBj:3dyl
PDBsum3dyl
PubMed18757755
UniProtO76083|PDE9A_HUMAN High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A (Gene Name=PDE9A)

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