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Hpgds complexed with an aza-quinoline

Analyse Hpgds complexed with an aza-quinoline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W58
Type: protein
Length: 398 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hematopoietic prostaglandin D synthase
EC: 5.3.99.2, 2.5.1.18
UniProt: O60760
Ligands: SWS, GSH
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 58% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hematopoietic prostaglandin D synthase (EC 5.3.99.2, 2.5.1.18)	protein	199	58% helix, 10% strand	O60760

Ligands and binding sites

SWS · 7-(azetidin-1-yl)-~{N}-[4-(2-oxidanylpropan-2-yl) cyclohexyl]-1,6-naphthyridine-3-carboxamide · ligand · 2 copies · chains A, B
GSH · Glutathione · ligand · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1010	0.75	0.77	82	GSH, SWS
2	154	0.65	0.86	27	empty
3	54	0.38	0.80	15	empty

Interfaces

1 interface between chains.

A–B · 1306 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

6W58 · hPGDS complexed with an aza-quinoline · the same entry in another collection · chain A against A, TM-score 1.00
O60760 · AlphaFold monomer V2.0 prediction for hematopoietic prostaglandin D synthase (O60760) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O60760
Elsewhere: RCSB PDB 6W58 · PDBe 6W58 · UniProt O60760

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