ISDA

Entry Detail

PDB ID:

5B4L

Keywords:

Title:

Crystal structure of the catalytic domain of human PDE10A complexed with 1-(cyclopropylmethyl)-5-(2-(2,3-dihydro-1H-imidazo[1,2-a]benzimidazol-1-yl)ethoxy)-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-4(1H)-one

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2016-04-05

Release Date:

2016-06-29

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.40 Å

R-Value Free:

0.28

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
Chain IDs:A, B
Chain Length:338
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q9Y233 EC:3.1.4.17

Ligand Molecules

6DW

Primary Citation

Design and synthesis of potent and selective pyridazin-4(1H)-one-based PDE10A inhibitors interacting with Tyr683 in the PDE10A selectivity pocket

Yoshikawa, M, Hitaka, T, Hasui, T, Fushimi, M, Kunitomo, J, Kokubo, H, Oki, H, Nakashima, K, Taniguchi, T.Show

Bioorg.Med.Chem. 24 3447 3455 (2016)

PMID: 27301679 DOI: 10.1016/j.bmc.2016.05.049

Abstact

Utilizing structure-based drug design techniques, we designed and synthesized phosphodiesterase 10A (PDE10A) inhibitors based on pyridazin-4(1H)-one. These compounds can interact with Tyr683 in the PDE10A selectivity pocket. Pyridazin-4(1H)-one derivative 1 was linked with a benzimidazole group through an alkyl spacer to interact with the OH of Tyr683 and fill the PDE10A selectivity pocket. After optimizing the linker length, we identified 1-(cyclopropylmethyl)-5-[3-(1-methyl-1H-benzimidazol-2-yl)propoxy]-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-4(1H)-one (16f) as having highly potent PDE10A inhibitory activity (IC50=0.76nM) and perfect selectivity against other PDEs (>13,000-fold, IC50=>10,000nM). The crystal structure of 16f bound to PDE10A revealed that the benzimidazole moiety was located deep within the PDE10A selectivity pocket and interacted with Tyr683. Additionally, a bidentate interaction existed between the 5-alkoxypyridazin-4(1H)-one moiety and the conserved Gln716 present in all PDEs.

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