6BOJ: CAMP-specific 3',5'-cyclic phosphodiesterase 4D

Crystal Structure of the PDE4D Catalytic Domain and UCR2 Regulatory Helix with BPN5004. Determined by X-ray diffraction at 1.7 Å resolution. Released 22 Aug 2018.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,021
Mol. weight: 172.7 kDa
Ligands: E31, MG, ZN
Released: 22 Aug 2018

Explore 6BOJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BOJ contains 97 α-helices and 8 β-strands across 4 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	255-262	8
α-helix	272-278	7
α-helix	283-294	12
α-helix	297-300	4
α-helix	305-317	13
α-helix	328-342	15
α-helix	345-347	3
α-helix	353-365	13
α-helix	375-380	6
α-helix	384-389	6
α-helix	394-405	12
α-helix	406-408	3
α-helix	420-435	16
α-helix	439-441	3
α-helix	442-454	13
β-strand	457-458	2	1
β-strand	464-465	2	1
α-helix	469-484	16
α-helix	487-489	3
α-helix	492-515	24
α-helix	518-521	4
α-helix	531-538	8
α-helix	539-543	5
α-helix	544-553	10
α-helix	559-574	16
α-helix	595-603	9

Chain B: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	255-262	8
α-helix	272-278	7
α-helix	283-294	12
α-helix	297-300	4
α-helix	305-317	13
α-helix	328-342	15
α-helix	345-347	3
α-helix	353-365	13
α-helix	375-380	6
α-helix	384-388	5
α-helix	394-405	12
α-helix	406-408	3
α-helix	420-435	16
α-helix	439-441	3
α-helix	442-454	13
β-strand	458	1	2
β-strand	464	1	2
α-helix	469-484	16
α-helix	487-489	3
α-helix	492-515	24
α-helix	518-521	4
α-helix	531-538	8
α-helix	539-543	5
α-helix	544-553	10
α-helix	559-574	16
α-helix	594-603	10

Chain C: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	255-262	8
α-helix	272-278	7
α-helix	283-294	12
α-helix	297-300	4
α-helix	305-317	13
α-helix	328-342	15
α-helix	345-347	3
α-helix	353-365	13
α-helix	375-380	6
α-helix	384-389	6
α-helix	394-405	12
α-helix	406-408	3
α-helix	420-435	16
α-helix	439-441	3
α-helix	442-454	13
β-strand	458	1	3
β-strand	464	1	3
α-helix	465	1
α-helix	469-484	16
α-helix	487-489	3
α-helix	492-515	24
α-helix	518-521	4
α-helix	531-538	8
α-helix	539-543	5
α-helix	544-553	10
α-helix	559-574	16
α-helix	594-603	10

Chain D: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	255-262	8
α-helix	272-278	7
α-helix	283-294	12
α-helix	297-300	4
α-helix	305-317	13
α-helix	328-342	15
α-helix	345-347	3
α-helix	353-365	13
α-helix	375-380	6
α-helix	384-389	6
α-helix	394-405	12
α-helix	406-408	3
α-helix	420-435	16
α-helix	439-441	3
α-helix	442-454	13
β-strand	458	1	4
β-strand	464	1	4
α-helix	469-484	16
α-helix	487-489	3
α-helix	492-515	24
α-helix	518-521	4
α-helix	531-538	8
α-helix	539-543	5
α-helix	544-553	10
α-helix	559-574	16
α-helix	594-603	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B, C, D	protein	370	Homo sapiens	Q07343 (AlphaFold model), Q08499 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6BOJ_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D (chains A, B, C, D)
MSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFK
IPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFA
SAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQ
RQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHC
ADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYI
VHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAPAPPLDEQNRDSQGNQVSEFISN
TFLDENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
E31	2-(4-{[2-(3-chlorophenyl)-6-ethylpyrimidin-4-yl]methyl}phenyl)acetamide	C21 H20 Cl N3 O	4
MG	Magnesium ion	Mg	4
ZN	Zinc ion	Zn	6

Water and common crystallization additives (MPD, CL) are not listed.

Primary citation

Memory enhancing effects of BPN14770, an allosteric inhibitor of phosphodiesterase-4D, in wild-type and humanized mice. Zhang, C., Xu, Y., Chowdhary, A. et al. Neuropsychopharmacology (2018) 43:2299-2309. DOI 10.1038/s41386-018-0178-6 · 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
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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