8OEG: PDE4B

PDE4B bound to MAPI compound 92a. Determined by X-ray diffraction at 1.89 Å resolution. Released 26 Apr 2023.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,881
Mol. weight: 49.26 kDa
Ligands: VL9, MG, ZN
Released: 26 Apr 2023

Explore 8OEG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8OEG contains 24 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: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	324-327	4
α-helix	335-342	8
α-helix	352-358	7
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4B	A	protein	421	Homo sapiens	Q07343 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8OEG_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4B (chains A)
MSVSEMASNKFKRMLNRELTHLSEMSRSGNQVSEYISNTFLDKQNDVEIPKVTAEEAPQP
MTQISGVKKLMHSSSLNNTSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPL
TCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLST
PALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGF
KLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVL
LLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMC
DKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
VL9	[(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-4-yl]-1-(3,4-dimethoxyphenyl)…	C36 H38 Cl2 N3 O7 S	1
MG	Magnesium ion	Mg	1
ZN	Zinc ion	Zn	1

Primary citation

Optimization of M 3 Antagonist-PDE4 Inhibitor (MAPI) Dual Pharmacology Molecules for the Treatment of COPD. Rizzi, A., Amari, G., Pivetti, F. et al. J Med Chem (2023) 66:11476-11497. DOI 10.1021/acs.jmedchem.3c01012 · 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
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
2QYL 1.95 Å, Crystal structure of PDE4B2B in complex with inhibitor NPV

Browse structure collections

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