MolNFT v1 · #147575 · protein
Crystal structure of mouse MTH1 mutant L116M with inhibitor TH588
6EHH · 7,8-dihydro-8-oxoguanine triphosphatase: “Crystal structure of mouse MTH1 mutant L116M with inhibitor TH588”. X-ray diffraction, 4 ligands (2GE, CU, MG), 6 pockets (best druggability 0.83). MolNFT v1 #147575 on GenesisL1: 3D…
- PDB
- 6EHH
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7,8-dihydro-8-oxoguanine triphosphatase
- EC
- 3.6.1.55, 3.6.1.56
- UniProt
- P53368
- Ligands
- 2GE, CU, MG, NO3
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 16% 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, 42% strand | P53368 |
| B, C | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 152 | 16% helix, 47% strand | P53368 |
| D | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 154 | 16% helix, 45% strand | P53368 |
Ligands and binding sites
- 2GE · N~4~-cyclopropyl-6-(2,3-dichlorophenyl)pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- CU · Copper (II) ion · metal · 4 copies · chains B, C, D
- MG · Magnesium ion · metal · chains C
- NO3 · Nitrate ion · ion · 19 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.83 | 0.86 | 77 | 2GE, NO3, GOL |
| 2 | 184 | 0.72 | 0.89 | 28 | 2GE, NO3 |
| 3 | 186 | 0.72 | 0.89 | 28 | 2GE, NO3 |
| 4 | 53 | 0.38 | 0.80 | 10 | NO3 |
| 5 | 101 | 0.34 | 0.73 | 25 | PEG |
Interfaces
4 interfaces between chains.
- A–B · 542 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 466 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 382 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 74 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EHH · Crystal structure of mouse MTH1 mutant L116M with inhibitor TH588 · the same entry in another collection · chain A against A, TM-score 1.00
- P53368 · AlphaFold monomer V2.0 prediction for 7,8-dihydro-8-oxoguanine triphosphatase (P53368) · a predicted model of the same protein · chain B 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 P53368
- Elsewhere: RCSB PDB 6EHH · PDBe 6EHH · UniProt P53368
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.