MolNFT v1 · #149864 · protein
Trypanosoma brucei PTR1 in complex with inhibitor 2B (F192)
6GCQ · Pteridine reductase: “Trypanosoma brucei PTR1 in complex with inhibitor 2B (F192)”. X-ray diffraction, 2 ligands (NAP, EUH), 7 pockets (best druggability 0.83). MolNFT v1 #149864 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6GCQ
- Type
- protein
- Length
- 1,006 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- UniProt
- O76290
- Ligands
- NAP, EUH
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase | protein | 251 | 47% helix, 15% strand | O76290 |
| B | Pteridine reductase | protein | 253 | 48% helix, 15% strand | O76290 |
| C | Pteridine reductase | protein | 252 | 47% helix, 15% strand | O76290 |
| 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
- EUH · 6-(trifluoromethylsulfanyl)-1,3-benzothiazol-2-amine · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.83 | 0.84 | 70 | empty |
| 2 | 619 | 0.78 | 0.83 | 48 | NAP, EUH, DMS |
| 3 | 609 | 0.77 | 0.83 | 50 | NAP, EUH, DMS |
| 4 | 579 | 0.77 | 0.83 | 48 | NAP, EUH, DMS |
| 5 | 556 | 0.76 | 0.83 | 49 | NAP, EUH, DMS |
Interfaces
6 interfaces between chains.
- B–D · 1880 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1863 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1427 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1403 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6GCQ · Trypanosoma brucei PTR1 in complex with inhibitor 2b (F192) · the same entry in another collection · chain D against D, 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 6GCQ · PDBe 6GCQ · UniProt O76290
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