Structure of PDB 3g4i Chain D Binding Site BS02

Receptor Information
>3g4i Chain D (length=334) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQE
RDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLST
PALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSV
LENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMN
LLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQL
YRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVH
PLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ
Ligand information
Ligand IDD71
InChIInChI=1S/C19H13N5O4/c25-18-16-5-2-8-21-17(16)23(14-3-1-4-15(11-14)24(27)28)19(26)22(18)12-13-6-9-20-10-7-13/h1-11H,12H2
InChIKeyYLHRMVRLIOIWTO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(cc(c1)[N+](=O)[O-])N2c3c(cccn3)C(=O)N(C2=O)Cc4ccncc4
CACTVS 3.341[O-][N+](=O)c1cccc(c1)N2C(=O)N(Cc3ccncc3)C(=O)c4cccnc24
ACDLabs 10.04[O-][N+](=O)c4cccc(N2c1ncccc1C(=O)N(C2=O)Cc3ccncc3)c4
FormulaC19 H13 N5 O4
Name1-(3-nitrophenyl)-3-(pyridin-4-ylmethyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL1232082
DrugBank
ZINCZINC000000598713
PDB chain3g4i Chain D Residue 904 [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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PDB3g4i Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H326 N487 T499 I502 F506 M523 S534 Q535 F538
Binding residue
(residue number reindexed from 1)		H82 N243 T255 I258 F262 M279 S290 Q291 F294
Annotation score1
Enzymatic activity
Enzyme Commision number 3.1.4.53: 3',5'-cyclic-AMP 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
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Biological Process
External links
PDB RCSB:3g4i, PDBe:3g4i, PDBj:3g4i
PDBsum3g4i
PubMed20037581
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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