MolNFT v1 · #163255 · protein
Leishmania major pteridine reductase 1 (LMPTR1) in complex with inhibitor 4 (nmt-C0026)
6RXC: “Leishmania major pteridine reductase 1 (LMPTR1) in complex with inhibitor 4 (nmt-C0026)”. X-ray diffraction, 2 ligands (NDP, KMK), 12 pockets (best druggability 0.81). MolNFT v1 #163255 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6RXC
- Type
- protein
- Length
- 1,041 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, KMK
- Pockets
- 12 · best druggability 0.81
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 | 263 | 48% helix, 16% strand | Q01782 |
| B | Pteridine reductase 1 (EC 1.5.1.33) | protein | 261 | 48% helix, 16% strand | Q01782 |
| C | Pteridine reductase 1 (EC 1.5.1.33) | protein | 261 | 46% helix, 16% strand | Q01782 |
| D | Pteridine reductase 1 (EC 1.5.1.33) | protein | 256 | 46% helix, 16% strand | Q01782 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- KMK · methyl 1-[4-[[2,4-bis(azanyl)pteridin-6-yl]methyl-(3-oxidanylpropyl)amino]phenyl]carbonylpiperidine-4-carboxylate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.81 | 0.83 | 78 | empty |
| 2 | 522 | 0.71 | 0.80 | 45 | NDP, KMK |
| 3 | 509 | 0.70 | 0.80 | 43 | NDP, KMK |
| 4 | 507 | 0.69 | 0.79 | 38 | NDP, KMK |
| 5 | 497 | 0.68 | 0.79 | 42 | NDP, KMK |
Interfaces
6 interfaces between chains.
- A–B · 1812 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1737 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1637 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1580 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 644 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6RXC · Leishmania major pteridine reductase 1 (LmPTR1) in complex with inhibitor 4 (NMT-C0026) · 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 6RXC · PDBe 6RXC · UniProt Q01782
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