2QYK: PDE4A10

Crystal structure of PDE4A10 in complex with inhibitor NPV. Determined by X-ray diffraction at 2.1 Å resolution. Released 8 Apr 2008.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,776
Mol. weight: 78.17 kDa
Ligands: MG, ZN, NPV
Released: 8 Apr 2008

Explore 2QYK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2QYK contains 48 α-helices and 4 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-307	7
α-helix	308-310	3
α-helix	318-324	7
α-helix	329-340	12
α-helix	343-346	4
α-helix	351-363	13
α-helix	374-388	15
α-helix	391-393	3
α-helix	399-411	13
α-helix	421-426	6
α-helix	430-434	5
α-helix	440-451	12
α-helix	452-454	3
α-helix	466-481	16
α-helix	485-487	3
α-helix	488-500	13
β-strand	504	1	1
β-strand	510	1	1
α-helix	515-530	16
α-helix	533-535	3
α-helix	538-561	24
α-helix	565-567	3
α-helix	577-584	8
α-helix	585-589	5
α-helix	590-599	10
α-helix	605-621	17

Chain B: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-307	7
α-helix	308-310	3
α-helix	318-324	7
α-helix	329-340	12
α-helix	343-346	4
α-helix	351-363	13
α-helix	374-388	15
α-helix	391-393	3
α-helix	399-411	13
α-helix	421-426	6
α-helix	430-434	5
α-helix	440-451	12
α-helix	452-454	3
α-helix	466-481	16
α-helix	485-487	3
α-helix	488-500	13
β-strand	504	1	2
β-strand	510	1	2
α-helix	515-530	16
α-helix	533-535	3
α-helix	538-562	25
α-helix	564-567	4
α-helix	577-584	8
α-helix	585-589	5
α-helix	590-600	11
α-helix	605-620	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclic AMP-specific phosphodiesterase HSPDE4A10	A, B	protein	335	Homo sapiens	P27815 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2QYK_1 Cyclic AMP-specific phosphodiesterase HSPDE4A10 (chains A, B)
HMNIPRFGVKTDQEELLAQELENLNKWGLNIFCVSDYAGGRSLTCIMYMIFQERDLLKKF
RIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVLLATPALDAVFTDLEILAALF
AAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEDNCDIFQNLSKR
QRQSLRKMVIDMVLATDMSKHMTLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLRNMVH
CADLSNPTKPLELYRQWTDRIMAEFFQQGDRERERGMEISPMCDKHTASVEKSQVGFIDY
IVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2
NPV	4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid	C21 H13 N3 O4	2

Primary citation

Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors. Wang, H., Peng, M.S., Chen, Y. et al. Biochem J (2007) 408:193-201. DOI 10.1042/BJ20070970 · PubMed

Other PDB entries of the same protein (UniProt P27815 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3HC8 1.79 Å, Investigation of Aminopyridiopyrazinones as PDE5 Inhibitors: Evaluation of Modifications…
3HDZ 1.8 Å, Identification, Synthesis, and SAR of Amino Substituted Pyrido[3,2b]pryaziones as Potent…
3I8V 2.25 Å, Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone
3TVX 2.84 Å, The structure of PDE4A with pentoxifylline at 2.84A resolution

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