MolNFT v1 · #88129 · protein
Structure of salmonella typhi type I dehydroquinase irreversibly inhibited with a 1,3,4-trihydroxyciclohexane-1-carboxylic acid derivative
4CLM · 3-dehydroquinate dehydratase: “Structure of salmonella typhi type I dehydroquinase irreversibly inhibited with a…”. X-ray diffraction, 3 ligands (WPL, LI, CL), 6 pockets (best druggability 0.69). MolNFT v1 #88129 on GenesisL1: 3D…
- PDB
- 4CLM
- Type
- protein
- Length
- 494 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-dehydroquinate dehydratase
- EC
- 4.2.1.10
- UniProt
- P24670
- Ligands
- WPL, LI, CL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 243 | 48% helix, 21% strand | P24670 |
| B | 3-dehydroquinate dehydratase (EC 4.2.1.10) | protein | 251 | 45% helix, 20% strand | P24670 |
Ligands and binding sites
- WPL · (1~{S},3~{S},4~{R},5~{R})-3-methyl-1,4,5-tris(hydroxyl)cyclohexane-1-carboxylic acid · ligand · chains B
- LI · Lithium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.96 | 19 | WPL |
| 2 | 192 | 0.50 | 0.77 | 23 | CL, LI |
| 3 | 92 | 0.41 | 0.78 | 19 | empty |
| 4 | 52 | 0.39 | 0.81 | 10 | empty |
| 5 | 82 | 0.39 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1082 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4CLM · Structure of Salmonella typhi type I dehydroquinase irreversibly inhibited with a… · the same entry in another collection · chain A against A, TM-score 1.00
- P24670 · AlphaFold monomer V2.0 prediction for 3-dehydroquinate dehydratase (P24670) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P24670
- Elsewhere: RCSB PDB 4CLM · PDBe 4CLM · UniProt P24670
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