5OHJ: Human phosphodiesterase 4B catalytic domain

Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor. Determined by X-ray diffraction at 1.6 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,699
Mol. weight: 98.52 kDa
Ligands: ZN, MG, 9VE
Released: 13 Dec 2017

Explore 5OHJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5OHJ contains 49 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	324-327	4
α-helix	335-342	8
α-helix	352-358	7
α-helix	363-374	12
α-helix	377-381	5
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	464-468	5
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	537-538	2	1
β-strand	544-545	2	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

Chain B: 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	464-468	5
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	2
β-strand	544	1	2
α-helix	549-564	16
α-helix	567-569	3
α-helix	572-596	25
α-helix	598-601	4
α-helix	606-608	3
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, B	protein	421	Homo sapiens	Q07343 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5OHJ_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4B (chains A, B)
MSVSEMASNKFKRMLNRELTHLSEMSRSGNQVSEYISNTFLDKQNDVEIPKVTAEEAPQP
MTQISGVKKLMHSSSLNNTSISRFGVNTENEDHLAKELEDLNKWGLNIFNVAGYSHNRPL
TCIMYAIFQERDLLKTFRISSDTFITYMMTLEDHYHSDVAYHNSLHAADVAQSTHVLLST
PALDAVFTDLEILAAIFAAAIHDVDHPGVSNQFLINTNSELALMYNDESVLENHHLAVGF
KLLQEEHCDIFMNLTKKQRQTLRKMVIDMVLATDMSKHMSLLADLKTMVETKKVTSSGVL
LLDNYTDRIQVLRNMVHCADLSNPTKSLELYRQWTDRIMEEFFQQGDKERERGMEISPMC
DKHTASVEKSQVGFIDYIVHPLWETWADLVQPDAQDILDTLEDNRNWYQSMIPQSHHHHH
H

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2
9VE	[(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-1-ium-4-yl]-1-[4-[bis(fluoran…	C32 H34 Cl2 F2 N3 O8 S	2

Primary citation

Discovery and Optimization of Thiazolidinyl and Pyrrolidinyl Derivatives as Inhaled PDE4 Inhibitors for Respiratory Diseases. Carzaniga, L., Amari, G., Rizzi, A. et al. J Med Chem (2017) 60:10026-10046. DOI 10.1021/acs.jmedchem.7b01044 · 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…
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
2QYL 1.95 Å, Crystal structure of PDE4B2B in complex with inhibitor NPV

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