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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
- 4RAQ
- Type
- protein
- Length
- 797 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypoxanthine-guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- P00492
- Ligands
- 3L8, MG
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 198 | 31% helix, 29% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 200 | 30% helix, 30% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 198 | 32% helix, 29% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 201 | 32% helix, 30% strand | P00492 |
Ligands and binding sites
- 3L8 · [(2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-phosphonoethyl)amino}ethoxy)methyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1178 | 0.83 | 0.84 | 68 | empty |
| 2 | 108 | 0.57 | 0.84 | 21 | empty |
| 3 | 235 | 0.53 | 0.76 | 26 | 3L8, MG |
| 4 | 217 | 0.51 | 0.76 | 25 | 3L8, MG |
| 5 | 224 | 0.50 | 0.75 | 26 | 3L8, MG |
Interfaces
6 interfaces between chains.
- B–D · 1614 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1572 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 903 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 338 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4RAQ · Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors… · 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 P00492
- Elsewhere: RCSB PDB 4RAQ · PDBe 4RAQ · UniProt P00492
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