MolNFT v1 · #153951 · protein
Crystal structure of human MTH1 in complex with compound MI1024
6JVP · 7,8-dihydro-8-oxoguanine triphosphatase: “Crystal structure of human MTH1 in complex with compound MI1024”. X-ray diffraction, 1 ligand (CJ9), 3 pockets (best druggability 0.74). MolNFT v1 #153951 on GenesisL1: 3D structure, binding…
- PDB
- 6JVP
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- 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
- P36639
- Ligands
- CJ9
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 43% 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 | 18% helix, 44% strand | P36639 |
| B | 7,8-dihydro-8-oxoguanine triphosphatase (EC 3.6.1.55, 3.6.1.56) | protein | 151 | 19% helix, 42% strand | P36639 |
Ligands and binding sites
- CJ9 · N4-cyclopropyl-6-piperidin-1-yl-pyrimidine-2,4-diamine · ligand · 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 | 185 | 0.74 | 0.90 | 31 | CJ9 |
| 2 | 191 | 0.72 | 0.89 | 30 | CJ9 |
| 3 | 69 | 0.31 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 482 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6JVP · Crystal structure of human MTH1 in complex with compound MI1024 · 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 0.98
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 6JVP · PDBe 6JVP · UniProt P36639
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