Research workbench
Crystal structure of zebrafish MTH1 in complex with TH588
Analyse Crystal structure of zebrafish MTH1 in complex with TH588 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HZX
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nudix (nucleoside diphosphate linked moiety X)-type motif 1
- UniProt
- Q7ZWC3
- Ligands
- 2GE, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nudix (nucleoside diphosphate linked moiety X)-type motif 1 | protein | 154 | 20% helix, 45% strand | Q7ZWC3 |
Ligands and binding sites
- 2GE · N~4~-cyclopropyl-6-(2,3-dichlorophenyl)pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- GOL · Glycerol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- ACT · Acetate ion · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.73 | 0.77 | 65 | ACT |
| 2 | 204 | 0.71 | 0.88 | 32 | 2GE, SO4 |
| 3 | 252 | 0.70 | 0.85 | 35 | 2GE, SO4 |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5HZX · Crystal structure of zebrafish MTH1 in complex with TH588 · the same entry in another collection · chain A 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 Q7ZWC3
- Elsewhere: RCSB PDB 5HZX · PDBe 5HZX · UniProt Q7ZWC3
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