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Receptor Information

>6fdi Chain D (length=324) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFKI
PVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTD
LEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVG
FKLLQEENCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMV
ETKKVTSSGVLLLDNYSDRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIM
EEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYIVHPLWETWADL
VHPDAQDILDTLEDNREWYQSTIP

Ligand ID

D5T

InChI

InChI=1S/C30H38N4O6/c1-30(2)16-25(35)33(26(36)17-30)18-27(37)32-13-11-20(12-14-32)34-29(38)22-8-6-5-7-21(22)28(31-34)19-9-10-23(39-3)24(15-19)40-4/h5-6,9-10,15,20-22H,7-8,11-14,16-18H2,1-4H3/t21-,22+/m0/s1

InChIKey

DZMHUZHTZIODAZ-FCHUYYIVSA-N

SMILES

Software	SMILES
CACTVS 3.385	COc1ccc(cc1OC)C2=NN(C3CCN(CC3)C(=O)CN4C(=O)CC(C)(C)CC4=O)C(=O)[CH]5CC=CC[CH]25
OpenEye OEToolkits 2.0.6	CC1(CC(=O)N(C(=O)C1)CC(=O)N2CCC(CC2)N3C(=O)C4CC=CCC4C(=N3)c5ccc(c(c5)OC)OC)C
OpenEye OEToolkits 2.0.6	CC1(CC(=O)N(C(=O)C1)CC(=O)N2CCC(CC2)N3C(=O)[C@@H]4CC=CC[C@@H]4C(=N3)c5ccc(c(c5)OC)OC)C
CACTVS 3.385	COc1ccc(cc1OC)C2=NN(C3CCN(CC3)C(=O)CN4C(=O)CC(C)(C)CC4=O)C(=O)[C@@H]5CC=CC[C@H]25

Formula

C30 H38 N4 O6

Name

1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione;
NPD-226

PDB chain

6fdi Chain D Residue 512 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6fdi hPDE4D2 structure with inhibitor NPD-226
Resolution	1.9 Å
Binding residue (original residue number in PDB)	M273 L319 I336 M357 Q369 F372
Binding residue (residue number reindexed from 1)	M186 L232 I249 M270 Q282 F285
Annotation score	1
Binding affinity	BindingDB: Ki=0.123027nM

Enzyme Commision number

3.1.4.53: 3',5'-cyclic-AMP phosphodiesterase.

	Molecular Function
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081	phosphoric diester hydrolase activity

	Biological Process
GO:0007165	signal transduction

PDB	RCSB:6fdi, PDBe:6fdi, PDBj:6fdi
PDBsum	6fdi
PubMed
UniProt	Q08499\|PDE4D_HUMAN 3',5'-cyclic-AMP phosphodiesterase 4D (Gene Name=PDE4D)

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Structure of PDB 6fdi Chain D Binding Site BS02