MolNFT v1 · #149878 · protein
Trypanosoma brucei PTR1 in complex with inhibitor 4C (F188)
6GD4 · Pteridine reductase: “Trypanosoma brucei PTR1 in complex with inhibitor 4C (F188)”. X-ray diffraction, 2 ligands (NAP, 6KT), 8 pockets (best druggability 0.83). MolNFT v1 #149878 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6GD4
- Type
- protein
- Length
- 1,000 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, 6KT
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Pteridine reductase | protein | 250 | 47% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- 6KT · 2-amino-1,3-benzothiazole-6-carboxamide · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.83 | 0.84 | 68 | empty |
| 2 | 622 | 0.77 | 0.83 | 48 | NAP, 6KT |
| 3 | 631 | 0.76 | 0.82 | 48 | NAP, 6KT |
| 4 | 614 | 0.75 | 0.81 | 48 | NAP, 6KT |
| 5 | 591 | 0.75 | 0.82 | 48 | NAP, 6KT |
Interfaces
6 interfaces between chains.
- B–D · 1897 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1872 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1428 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1419 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 561 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6GD4 · Trypanosoma brucei PTR1 in complex with inhibitor 4c (F188) · 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 O76290
- Elsewhere: RCSB PDB 6GD4 · PDBe 6GD4 · UniProt O76290
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