Structure of PDB 3g4g Chain D Binding Site BS03

Receptor Information
>3g4g Chain D (length=337) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NQVSEFISNTFLDEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTI
FQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVL
LSTPALEAVFTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYND
SSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSK
HMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKP
LQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDY
IVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQ
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 chain3g4g 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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PDB3g4g Design of phosphodiesterase 4D (PDE4D) allosteric modulators for enhancing cognition with improved safety.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F196 H326 N487 T499 I502 F506 S534 Q535 F538
Binding residue
(residue number reindexed from 1)		F6 H85 N246 T258 I261 F265 S293 Q294 F297
Annotation score1
Binding affinityMOAD: ic50=19nM
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:3g4g, PDBe:3g4g, PDBj:3g4g
PDBsum3g4g
PubMed20037581
UniProtQ08499|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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