Research workbench
Crystal structure of human MTH1 in complex with compound MI1016
Analyse Crystal structure of human MTH1 in complex with compound MI1016 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JVM
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.098
- Source
- Homo sapiens
- Molecule
- 7,8-dihydro-8-oxoguanine triphosphatase
- EC
- 3.6.1.55, 3.6.1.56
- UniProt
- P36639
- Ligands
- CGX
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.098 · 2 distinct chains · 17% 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 | 16% helix, 45% 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
- CGX · N4-cyclopropyl-5-ethyl-6-piperidin-1-yl-pyrimidine-2,4-diamine · ligand · chains A
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 | 231 | 0.73 | 0.87 | 32 | empty |
| 2 | 233 | 0.72 | 0.87 | 35 | CGX |
| 3 | 72 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6JVM · Crystal structure of human MTH1 in complex with compound MI1016 · 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 6JVM · PDBe 6JVM · UniProt P36639
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