1Y2K: Catalytic Domain Of Human Phosphodiesterase 4D

Catalytic Domain Of Human Phosphodiesterase 4D In Complex With 3,5-dimethyl-1-(3-nitro-phenyl)-1H-pyrazole-4-carboxylic acid ethyl ester. Determined by X-ray diffraction at 1.36 Å resolution. Released 1 Mar 2005.

Method: X-ray diffraction
Resolution: 1.36 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,927
Mol. weight: 83 kDa
Ligands: 7DE, MG, ZN
Released: 1 Mar 2005

Explore 1Y2K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1Y2K contains 47 α-helices and 2 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	87-95	9
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	1
β-strand	298	1	1
α-helix	303-318	16
α-helix	321-323	3
α-helix	326-350	25
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: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	87-96	10
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
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	393-409	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
cAMP-specific 3',5'-cyclic phosphodiesterase 4D	A, B	protein	349	Homo sapiens	Q08499 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1Y2K_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D (chains A, B)
MGSSHHHHHHSSGLVPRGSHMTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHT
IFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAV
FTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEE
NCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYS
DRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNAS
VEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQS

Ligands and cofactors

ID	Name	Formula	Copies
7DE	3,5-dimethyl-1-(3-nitrophenyl)-1H-pyrazole-4-carboxylic acid ethyl ester	C14 H15 N3 O4	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	2

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

Primary citation

A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Card, G.L., Blasdel, L., England, B.P. et al. Nat Biotechnol (2005) 23:201-207. DOI 10.1038/nbt1059 · PubMed

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

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
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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