3I8V: CAMP-specific 3',5'-cyclic phosphodiesterase 4A

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone. Determined by X-ray diffraction at 2.25 Å resolution. Released 21 Jul 2009.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,833
Mol. weight: 82.45 kDa
Ligands: CO, 0MO, MG, ZN
Released: 21 Jul 2009

Explore 3I8V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3I8V contains 47 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	301-308	8
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	503-504	2	1
β-strand	510-511	2	1
α-helix	515-530	16
α-helix	533-535	3
α-helix	538-562	25
α-helix	564-567	4
α-helix	572-574	3
α-helix	577-584	8
α-helix	585-589	5
α-helix	590-600	11
α-helix	605-620	16

Chain B: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	301-308	8
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	538-561	24
α-helix	564-567	4
α-helix	577-584	8
α-helix	585-589	5
α-helix	590-599	10
α-helix	605-620	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4A	A, B	protein	354	Homo sapiens	P27815 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3I8V_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4A (chains A, B)
MGSSHHHHHHSSGLVPRGSHMNIPRFGVKTDQEELLAQELENLNKWGLNIFCVSDYAGGR
SLTCIMYMIFQERDLLKKFRIPVDTMVTYMLTLEDHYHADVAYHNSLHAADVLQSTHVLL
ATPALDAVFTDLEILAALFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAV
GFKLLQEDNCDIFQNLSKRQRQSLRKMVIDMVLATDMSKHMTLLADLKTMVETKKVTSSG
VLLLDNYSDRIQVLRNMVHCADLSNPTKPLELYRQWTDRIMAEFFQQGDRERERGMEISP
MCDKHTASVEKSQVGFIDYIVHPLWETWADLVHPDAQEILDTLEDNRDWYYSAI

Ligands and cofactors

ID	Name	Formula	Copies
CO	Cobalt (II) ion	Co	1
0MO	(4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one	C15 H22 N2 O3	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

Crystal structure of human PDE4a with 4-(3-butoxy-4-methoxyphenyl)methyl-2-imidazolidone. Cheng, R.K.Y., Crawley, L., Barker, J. et al. To be published.

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…
2QYK 2.1 Å, Crystal structure of PDE4A10 in complex with inhibitor NPV
3TVX 2.84 Å, The structure of PDE4A with pentoxifylline at 2.84A resolution

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