MolNFT v1 · #54057 · protein
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
2XDA · 3-dehydroquinate dehydratase: “Structure of helicobacter pylori type II dehydroquinase in complex with inhibitor compound…”. X-ray diffraction, 1 ligand (JPS), 1 pocket (best druggability 0.56). MolNFT v1 #54057 on GenesisL1: 3D…
- 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.
| Volume (ų) | 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
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 Q48255
- Elsewhere: RCSB PDB 2XDA · PDBe 2XDA · UniProt Q48255
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