3O0J: PDE4B

PDE4B In complex with ligand an2898. Determined by X-ray diffraction at 1.95 Å resolution. Released 10 Aug 2011.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,896
Mol. weight: 38.55 kDa
Ligands: 3OJ, MG, ZN
Released: 10 Aug 2011

Explore 3O0J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3O0J contains 23 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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	163-170	8
α-helix	180-186	7
α-helix	191-202	12
α-helix	205-208	4
α-helix	213-225	13
α-helix	236-250	15
α-helix	253-255	3
α-helix	261-273	13
α-helix	283-288	6
α-helix	292-296	5
α-helix	302-313	12
α-helix	314-316	3
α-helix	328-343	16
α-helix	347-349	3
α-helix	350-362	13
β-strand	366	1	1
β-strand	372	1	1
α-helix	377-392	16
α-helix	395-397	3
α-helix	400-423	24
α-helix	426-429	4
α-helix	439-446	8
α-helix	447-451	5
α-helix	452-462	11
α-helix	467-482	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	protein	323	Homo sapiens	Q07343 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3O0J_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4B (chains A)
NEDHLAKELEDLNKWGLNIFNVAGYSHNRPLTCIMYAIFQERDLLKTFRISSDTFITYMM
TLEDHYHSDVAYHNSLHAADVAQSTHVLLSTPALDAVFTDLEILAAIFAAAIHDVDHPGV
SNQFLINTNSELALMYNDESVLENHHLAVGFKLLQEEHCDIFMNLTKKQRQTLRKMVIDM
VLATDMSKHMSLLADLKTMVETKKVTSSGVLLLDNYTDRIQVLRNMVHCADLSNPTKSLE
LYRQWTDRIMEEFFQQGDKERERGMEISPMCDKHTASVEKSQVGFIDYIVHPLWETWADL
VQPDAQDILDTLEDNRNWYQSMI

Ligands and cofactors

ID	Name	Formula	Copies
3OJ	4-[(1-hydroxy-1,3-dihydro-2,1-benzoxaborol-5-yl)oxy]benzene-1,2-dicarbonitrile	C15 H9 B N2 O3	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

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

Primary citation

Boron-based phosphodiesterase inhibitors show novel binding of boron to PDE4 bimetal center. Freund, Y.R., Akama, T., Alley, M.R. et al. FEBS Lett (2012) 586:3410-3414. DOI 10.1016/j.febslet.2012.07.058 · 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
4MYQ 1.9 Å, Selective Inhibition of the Catalytic Domain Of Human Phosphodiesterase 4B With A-33
1XM6 1.92 Å, Catalytic Domain Of Human Phosphodiesterase 4B In Complex With (R)-Mesopram

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