MolNFT v1 · #125286 · protein
Leishmania major pteridine reductase 1 (PTR1) in complex with compound 1
5L4N: “Leishmania major pteridine reductase 1 (PTR1) in complex with compound 1”. X-ray diffraction, 2 ligands (NDP, 6QT), 11 pockets (best druggability 0.82). MolNFT v1 #125286 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5L4N
- Type
- protein
- Length
- 1,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase 1
- EC
- 1.5.1.33
- UniProt
- Q01782
- Ligands
- NDP, 6QT
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase 1 (EC 1.5.1.33) | protein | 254 | 47% helix, 17% strand | Q01782 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 254 | 47% helix, 16% strand | Q01782 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 265 | 48% helix, 15% strand | Q01782 |
| D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 264 | 47% helix, 16% strand | Q01782 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 6QT · (2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one · ligand · 2 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains D
- GOL · Glycerol · additive · chains A, C
- ACT · Acetate ion · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
- PGE · Triethylene glycol · additive · chains B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.82 | 0.84 | 83 | empty |
| 2 | 634 | 0.72 | 0.79 | 63 | NDP |
| 3 | 563 | 0.71 | 0.80 | 42 | NDP |
| 4 | 516 | 0.69 | 0.79 | 55 | 6QT, NDP |
| 5 | 466 | 0.69 | 0.80 | 42 | 6QT, NDP |
Interfaces
6 interfaces between chains.
- C–D · 1765 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1687 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1607 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 1597 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 650 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5L4N · Leishmania major Pteridine reductase 1 (PTR1) in complex with compound 1 · 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 Q01782
- Elsewhere: RCSB PDB 5L4N · PDBe 5L4N · UniProt Q01782
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