6IMD: PDE4D

Crystal structure of PDE4D complexed with a novel inhibitor. Determined by X-ray diffraction at 1.5 Å resolution. Released 23 Oct 2019.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,730
Mol. weight: 81.55 kDa
Ligands: AH9, MG, ZN
Released: 23 Oct 2019

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

Secondary structure: helices and β-sheets

6IMD contains 46 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	88-96	9
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: 23 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	90-96	7
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	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	393-408	16

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

>6IMD_1 cAMP-specific 3',5'-cyclic phosphodiesterase 4D (chains A, B)
MGSSHHHHHHSSGLVPRGSHMTEQEDVLAKELEDVNKWGLHVFRIAELSGNRPLTVIMHT
IFQERDLLKTFKIPVDTLITYLMTLEDHYHADVAYHNNIHAADVVQSTHVLLSTPALEAV
FTDLEILAAIFASAIHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEE
NCDIFQNLTKKQRQSLRKMVIDIVLATDMSKHMNLLADLKTMVETKKVTSSGVLLLDNYS
DRIQVLQNMVHCADLSNPTKPLQLYRQWTDRIMEEFFRQGDRERERGMEISPMCDKHNAS
VEKSQVGFIDYIVHPLWETWADLVHPDAQDILDTLEDNREWYQSTIPQS

Ligands and cofactors

ID	Name	Formula	Copies
AH9	6,7-dimethoxy-3,4-dihydroisoquinoline-2(1H)-carbaldehyde	C12 H15 N O3	2
MG	Magnesium ion	Mg	4
ZN	Zinc ion	Zn	2

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

Primary citation

Structure-Aided Identification and Optimization of Tetrahydro-isoquinolines as Novel PDE4 Inhibitors Leading to Discovery of an Effective Antipsoriasis Agent. Zhang, X., Dong, G., Li, H. et al. J Med Chem (2019) 62:5579-5593. DOI 10.1021/acs.jmedchem.9b00518 · 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
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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