MolNFT v1 · #105626 · protein
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
4RAC · Hypoxanthine-guanine phosphoribosyltransferase: “Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors of the human…”. X-ray diffraction, 2 ligands (3L4, MG), 14 pockets (best druggability 0.84).…
- PDB
- 4RAC
- Type
- protein
- Length
- 805 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
- 3L4, MG
- Pockets
- 14 · best druggability 0.84
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 | 204 | 31% helix, 29% strand | P00492 |
| B | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 200 | 32% helix, 31% strand | P00492 |
| C | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 203 | 31% helix, 30% strand | P00492 |
| D | Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 198 | 30% helix, 30% strand | P00492 |
Ligands and binding sites
- 3L4 · [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl) ethyl][(e)-2-phosphonoethenyl]amino}ethoxy) methyl]phosphonic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.84 | 0.85 | 81 | empty |
| 2 | 347 | 0.65 | 0.80 | 30 | 3L4, MG |
| 3 | 69 | 0.64 | 0.92 | 22 | empty |
| 4 | 258 | 0.56 | 0.78 | 27 | 3L4, MG |
| 5 | 261 | 0.56 | 0.77 | 29 | 3L4, MG |
Interfaces
6 interfaces between chains.
- A–C · 1678 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1642 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 873 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 817 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 356 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4RAC · Aza-acyclic nucleoside phosphonates containing a second phosphonate group as inhibitors… · the same entry in another collection · chain D against D, TM-score 1.00
- P00492 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine phosphoribosyltransferase… · a predicted model of the same protein · chain D 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 P00492
- Elsewhere: RCSB PDB 4RAC · PDBe 4RAC · UniProt P00492
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