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Structure of helicobacter pylori type II dehydroquinase in complex with inhibitor compound (4R,6R,7S)-2-(2-CYCLOPROPYL)ETHYL-4,6,7- trihydroxy-4,5,6,7-TETRAHYDROBENZO(B)THIOPHENE-4-carboxylic acid

Analyse Structure of helicobacter pylori type II dehydroquinase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2XDA
Type: protein
Length: 150 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-dehydroquinate dehydratase
EC: 4.2.1.10
UniProt: Q48255
Ligands: JPS
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	150	47% helix, 19% strand	Q48255

Ligands and binding sites

JPS · (4R,6R,7S)-2-(2-cyclopropylethyl)-4,6,7-trihydroxy-4,5,6,7-tetrahydro-1-benzothiophene-4-carboxylic acid · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	129	0.56	0.83	19	JPS

Compared structures

2XDA · STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR… · the same entry in another collection · chain A against A, TM-score 1.00
Q48255 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (Q48255) · a predicted model of the same protein · chain A against A, TM-score 0.99

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Every structure of UniProt Q48255
Elsewhere: RCSB PDB 2XDA · PDBe 2XDA · UniProt Q48255

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