Research workbench
Crystal structure of human MTH1 in complex with compound MI0861
Analyse Crystal structure of human MTH1 in complex with compound MI0861 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JVI
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.249
- Source
- Homo sapiens
- Molecule
- 7,8-dihydro-8-oxoguanine triphosphatase
- EC
- 3.6.1.55, 3.6.1.56
- UniProt
- P36639
- Ligands
- 95R, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.249 · 2 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 154 | 19% helix, 47% strand | P36639 |
| B | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 151 | 19% helix, 44% strand | P36639 |
Ligands and binding sites
- 95R · (4R)-4-(2-methoxyphenyl)-4,6,7,8-tetrahydroquinoline-2, 5(1H,3H)-dione · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.73 | 0.86 | 34 | 95R |
| 2 | 242 | 0.72 | 0.86 | 26 | 95R |
| 3 | 66 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 445 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6JVI · Crystal structure of human MTH1 in complex with compound MI0861 · the same entry in another collection · chain A against A, TM-score 1.00
- P36639 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P36639) · 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 P36639
- Elsewhere: RCSB PDB 6JVI · PDBe 6JVI · UniProt P36639
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