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Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human, plasmodium falciparum and vivax 6- oxopurine phosphoribosyltransferases and their pro-drugs as antimalarial agents
Analyse Aza-acyclic nucleoside phosphonates containing a second phosphonate group as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RAD
- Type
- protein
- Length
- 1,619 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- P00492
- Ligands
- 3L5, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 197 | 30% helix, 29% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 207 | 30% helix, 30% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 202 | 32% helix, 30% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 202 | 30% helix, 29% strand | P00492 |
| E | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 206 | 31% helix, 32% strand | P00492 |
| F | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 197 | 29% helix, 31% strand | P00492 |
| G | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 200 | 31% helix, 31% strand | P00492 |
| H | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 208 | 29% helix, 31% strand | P00492 |
Ligands and binding sites
- 3L5 · (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl) ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl) phosphonic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 9 copies · chains A, B, C, D, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1073 | 0.85 | 0.87 | 88 | empty |
| 2 | 1189 | 0.83 | 0.84 | 84 | empty |
| 3 | 150 | 0.60 | 0.84 | 25 | empty |
| 4 | 360 | 0.60 | 0.77 | 31 | 3L5, MG |
| 5 | 217 | 0.59 | 0.80 | 31 | empty |
Interfaces
17 interfaces between chains.
- E–G · 1766 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1742 Ų buried · 28 hydrogen bonds · protein-protein
- B–D · 1709 Ų buried · 27 hydrogen bonds · protein-protein
- F–H · 1678 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 878 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4RAD · Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors… · the same entry in another collection · chain H against H, TM-score 1.00
- P00492 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · 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 P00492
- Elsewhere: RCSB PDB 4RAD · PDBe 4RAD · UniProt P00492
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