Research workbench
Selective screening and design to identify inhibitors of leishmania major pteridine reductase 1
Analyse Selective screening and design to identify inhibitors of leishmania major… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H4V
- Type
- protein
- Length
- 2,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase 1
- EC
- 1.5.1.33
- UniProt
- Q01782
- Ligands
- NAP, DVP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase 1 (EC 1.5.1.33) | protein | 273 | 45% helix, 14% strand | Q01782 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 273 | 46% helix, 14% strand | Q01782 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 259 | 46% helix, 16% strand | Q01782 |
| D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 263 | 46% helix, 16% strand | Q01782 |
| E | Pteridine reductase 1 (EC 1.5.1.33) | protein | 266 | 46% helix, 15% strand | Q01782 |
| F | Pteridine reductase 1 (EC 1.5.1.33) | protein | 270 | 46% helix, 14% strand | Q01782 |
| G | Pteridine reductase 1 (EC 1.5.1.33) | protein | 261 | 45% helix, 15% strand | Q01782 |
| H | Pteridine reductase 1 (EC 1.5.1.33) | protein | 263 | 46% helix, 17% strand | Q01782 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- DVP · Methyl 1-(4-{[(2,4-diaminopteridin-6-yl)methyl]amino}benzoyl)piperidine-4-carboxylate · ligand · 8 copies · chains A, D, B, C, E, H, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1190 | 0.82 | 0.84 | 89 | empty |
| 2 | 1200 | 0.82 | 0.83 | 79 | empty |
| 3 | 690 | 0.73 | 0.79 | 64 | NAP, DVP |
| 4 | 627 | 0.73 | 0.80 | 50 | NAP, DVP |
| 5 | 519 | 0.72 | 0.81 | 44 | NAP, DVP |
Interfaces
14 interfaces between chains.
- E–F · 2032 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1981 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1978 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1963 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1646 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3H4V · Selective screening and design to identify inhibitors of leishmania major pteridine… · the same entry in another collection · chain H against H, TM-score 1.00
- Q01782 · AlphaFold monomer V2.0 prediction for pteridine reductase 1 (Q01782) · a predicted model of the same protein · chain C 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 Q01782
- Elsewhere: RCSB PDB 3H4V · PDBe 3H4V · UniProt Q01782
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