Structure of PDB 3g4i Chain A Binding Site BS02

Receptor Information
>3g4i Chain A (length=331) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDL
LKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPAL
EAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLEN
HHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLA
DLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQ
WTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLW
ETWADLVHPDAQDILDTLEDNREWYQSTIPQ
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 A Residue 901 [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 T499 I502 M503 M523 S534 Q535 F538
Binding residue
(residue number reindexed from 1)		H79 T252 I255 M256 M276 S287 Q288 F291
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=9.04,IC50=0.91nM
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
View graph for
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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