7B9H: PDE4D catalytic domain

Crystal structure of the PDE4D catalytic domain in complex with GEBR-42a. Determined by X-ray diffraction at 1.5 Å resolution. Released 30 Jun 2021.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,328
Mol. weight: 82.09 kDa
Ligands: T3K, MG, ZN
Released: 30 Jun 2021

Explore 7B9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7B9H 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	89-96	8
α-helix	106-112	7
α-helix	117-128	12
α-helix	131-135	5
α-helix	139-151	13
α-helix	162-176	15
α-helix	179-181	3
α-helix	187-199	13
α-helix	209-214	6
α-helix	218-223	6
α-helix	228-239	12
α-helix	240-242	3
α-helix	254-269	16
α-helix	273-275	3
α-helix	276-288	13
β-strand	292	1	1
β-strand	298	1	1
α-helix	303-318	16
α-helix	321-323	3
α-helix	326-349	24
α-helix	352-355	4
α-helix	365-372	8
α-helix	373-377	5
α-helix	378-387	10
α-helix	393-408	16

Chain B: 24 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	89-95	7
α-helix	96-98	3
α-helix	106-112	7
α-helix	117-128	12
α-helix	131-134	4
α-helix	139-151	13
α-helix	162-176	15
α-helix	179-181	3
α-helix	187-199	13
α-helix	209-214	6
α-helix	218-223	6
α-helix	228-239	12
α-helix	240-242	3
α-helix	254-269	16
α-helix	273-275	3
α-helix	276-288	13
β-strand	292	1	2
β-strand	298	1	2
α-helix	303-318	16
α-helix	321-323	3
α-helix	326-349	24
α-helix	352-355	4
α-helix	365-372	8
α-helix	373-377	5
α-helix	378-387	10
α-helix	393-407	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

>7B9H_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D (chains A, B)
MSIPRFGVKTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHTIFQERDLLKTFK
IPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAVFTDLEILAAIFA
SAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQ
RQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYSDRIQVLQNMVHC
ADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNASVEKSQVGFIDYI
VHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
T3K	3-[(~{E})-1-(3-cyclopentyloxy-4-methoxy-phenyl)ethylideneamino]oxy-1-morpholin-…	C21 H30 N2 O5	2
MG	Magnesium ion	Mg	8
ZN	Zinc ion	Zn	2

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

Primary citation

Design, synthesis, biological evaluation and structural characterization of novel GEBR library PDE4D inhibitors. Brullo, C., Rapetti, F., Abbate, S. et al. Eur J Med Chem (2021) 223:113638-113638. DOI 10.1016/j.ejmech.2021.113638 · 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…
6FDC 1.45 Å, Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a
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
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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