6FDC: PDE4D catalytic domain

Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a. Determined by X-ray diffraction at 1.45 Å resolution. Released 16 May 2018.

Method: X-ray diffraction
Resolution: 1.45 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,925
Mol. weight: 80.5 kDa
Ligands: ZN, MG, DD5, D5N
Released: 16 May 2018

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

Secondary structure: helices and β-sheets

6FDC contains 47 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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	258-262	5
α-helix	272-278	7
α-helix	283-294	12
α-helix	297-301	5
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	1
β-strand	464	1	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

Chain B: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	257-261	5
α-helix	262-264	3
α-helix	272-278	7
α-helix	283-294	12
α-helix	297-301	5
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	559-573	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B	protein	343	Homo sapiens	Q08499 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6FDC_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D (chains A, B)
MSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFK
IPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFA
SAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQ
RQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHC
ADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYI
VHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	5
DD5	(2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3…	C22 H29 F2 N3 O4	1
D5N	(2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3…	C22 H29 F2 N3 O4	1

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

Primary citation

Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Prosdocimi, T., Mollica, L., Donini, S. et al. Biochemistry (2018) 57:2876-2888. DOI 10.1021/acs.biochem.8b00288 · PubMed

Other PDB entries of the same protein (UniProt Q08499 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1Y2K 1.36 Å, Catalytic Domain Of Human Phosphodiesterase 4D In Complex With…
8W4R 1.37 Å, Crystal structure of PDE4D complexed with CVT-313
1Y2B 1.4 Å, Catalytic Domain Of Human Phosphodiesterase 4D In Complex With…
6LRM 1.45 Å, Crystal structure of PDE4D catalytic domain in complex with arctigenin
6IMI 1.46 Å, Crystal structure of PDE4D complexed with a novel inhibitor
6IMT 1.48 Å, Crystal structure of PDE4D complexed with a novel inhibitor
6IMD 1.5 Å, Crystal structure of PDE4D complexed with a novel inhibitor
7B9H 1.5 Å, Crystal structure of the PDE4D catalytic domain in complex with GEBR-42a
7CBJ 1.5 Å, Crystal structure of PDE4D catalytic domain in complex with compound 36
6IMR 1.5 Å, Crystal structure of PDE4D complexed with a novel inhibitor
1XOR 1.54 Å, Catalytic Domain Of Human Phosphodiesterase 4D In Complex With Zardaverine
7YQF 1.54 Å, Crystal structure of PDE4D complexed with glycyrrhisoflavone

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