MolNFT v1 · #99509 · protein
The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
4M5K · 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine…: “The identification, analysis and structure-based development of novel inhibitors of…”. X-ray diffraction, 3 ligands (APC, YH3, CA), 2 pockets (best druggability 0.63). MolNFT v1…
- PDB
- 4M5K
- Type
- protein
- Length
- 159 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
- EC
- 2.7.6.3
- UniProt
- P26281
- Ligands
- APC, YH3, CA
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase (EC 2.7.6.3) | protein | 159 | 30% helix, 27% strand | P26281 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- YH3 · 2-amino-8-{[2-(3-methylphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.63 | 0.79 | 42 | APC, CA, YH3, GOL |
| 2 | 53 | 0.32 | 0.77 | 14 | empty |
Compared structures
- 4M5K · The Identification, Analysis and Structure-Based Development of Novel Inhibitors of… · 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 P26281
- Elsewhere: RCSB PDB 4M5K · PDBe 4M5K · UniProt P26281
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.