4MYQ: CAMP-specific 3',5'-cyclic phosphodiesterase 4B

Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33. Determined by X-ray diffraction at 1.9 Å resolution. Released 1 Jan 2014.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,223
Mol. weight: 43.5 kDa
Ligands: ZN, MG, 19T
Released: 1 Jan 2014

Explore 4MYQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4MYQ contains 25 α-helices and 2 β-strands across 1 chain. 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: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	325-328	4
α-helix	335-342	8
α-helix	352-357	6
α-helix	363-374	12
α-helix	377-380	4
α-helix	385-397	13
α-helix	408-422	15
α-helix	425-427	3
α-helix	433-445	13
α-helix	455-460	6
α-helix	464-469	6
α-helix	474-485	12
α-helix	486-488	3
α-helix	500-515	16
α-helix	519-521	3
α-helix	522-534	13
β-strand	538	1	1
β-strand	544	1	1
α-helix	549-564	16
α-helix	567-569	3
α-helix	572-595	24
α-helix	598-601	4
α-helix	611-618	8
α-helix	619-623	5
α-helix	624-633	10
α-helix	639-654	16
α-helix	672-676	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	protein	372	Homo sapiens	Q07343 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4MYQ_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4B (chains A)
GSHMSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLK
TFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAA
IFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLT
KKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNM
VHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFI
DYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSPSPPLDEQNRDCQGLMEKFQ
FELTLDEEDSEG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MG	Magnesium ion	Mg	1
19T	(4-{[2-(5-chlorothiophen-2-yl)-5-ethyl-6-methylpyrimidin-4-yl]amino}phenyl)acet…	C19 H18 Cl N3 O2 S	1

Water and common crystallization additives (EDO, NA) are not listed.

Primary citation

Structural basis for the design of selective phosphodiesterase 4B inhibitors. Fox, D., Burgin, A.B., Gurney, M.E. Cell Signal (2014) 26:657-663. DOI 10.1016/j.cellsig.2013.12.003 · PubMed

Other PDB entries of the same protein (UniProt Q07343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4KP6 1.5 Å, Crystal structure of human phosphodiesterase 4B (PDE4B) in complex with a…
2CHM 1.6 Å, Crystal structure of N2 substituted pyrazolo pyrimidinones - a flipped binding mode in…
5OHJ 1.6 Å, Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor.
3FRG 1.7 Å, Catalytic Domain of Human Phosphodiesterase 4B2B in Complex with a Quinoline Inhibitor
6BOJ 1.7 Å, Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004
3D3P 1.75 Å, Crystal structure of PDE4B catalytic domain in complex with a pyrazolopyridine inhibitor
3GWT 1.75 Å, Catalytic domain of human phosphodiesterase 4B2B in complex with a quinoline inhibitor
1F0J 1.77 Å, Catalytic domain of human phosphodiesterase 4B2B
5K6J 1.86 Å, Human Phospodiesterase 4B in complex with pyridyloxy-benzoxaborole based inhibitor
8OEG 1.89 Å, PDE4B bound to MAPI compound 92a
1XM6 1.92 Å, Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Mesopram
2QYL 1.95 Å, Crystal structure of PDE4B2B in complex with inhibitor NPV

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