5YWX image
Entry Detail
PDB ID:
5YWX
Title:
Crystal structure of hematopoietic prostaglandin D synthase in complex with F092
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2017-11-30
Release Date:
2018-09-05
Method Details:
Experimental Method:
Resolution:
1.74 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Hematopoietic prostaglandin D synthase
Chain IDs:A, B, C, D
Chain Length:198
Number of Molecules:4
Biological Source:Homo sapiens
Primary Citation
Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies.
Bioorg. Med. Chem. 26 4726 4734 (2018)
PMID: 30121213 DOI: 10.1016/j.bmc.2018.08.014

Abstact

Hematopoietic prostaglandin D synthase (H-PGDS) is one of the two enzymes that catalyze prostaglandin D2 synthesis and a potential therapeutic target of allergic and inflammatory responses. To reveal key molecular interactions between a high-affinity ligand and H-PGDS, we designed and synthesized a potent new inhibitor (KD: 0.14 nM), determined the crystal structure in complex with human H-PGDS, and quantitatively analyzed the ligand-protein interactions by the fragment molecular orbital calculation method. In the cavity, 10 water molecules were identified, and the interaction energy calculation indicated their stable binding to the surface amino acids in the cavity. Among them, 6 water molecules locating from the deep inner cavity to the peripheral part of the cavity contributed directly to the ligand binding by forming hydrogen bonding interactions. Arg12, Gly13, Gln36, Asp96, Trp104, Lys112 and an essential co-factor glutathione also had strong interactions with the ligand. A strong repulsive interaction between Leu199 and the ligand was canceled out by forming a hydrogen bonding network with the adjacent conserved water molecule. Our quantitative studies including crystal water molecules explained that compounds with an elongated backbone structure to fit from the deep inner cavity to the peripheral part of the cavity would have strong affinity to human H-PGDS.

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