MolNFT v1 · #53927 · protein
High resolution structure of TBPTR1 in complex with pemetrexed
2X9G · Pteridine reductase: “High resolution structure of TBPTR1 in complex with pemetrexed”. X-ray diffraction, 2 ligands (NAP, LYA), 11 pockets (best druggability 0.84). MolNFT v1 #53927 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2X9G
- Type
- protein
- Length
- 1,002 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pteridine reductase
- EC
- 1.5.1.33
- UniProt
- O76290
- Ligands
- NAP, LYA
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pteridine reductase (EC 1.5.1.33) | protein | 251 | 48% helix, 15% strand | O76290 |
| B | Pteridine reductase (EC 1.5.1.33) | protein | 250 | 47% helix, 14% strand | O76290 |
| C | Pteridine reductase (EC 1.5.1.33) | protein | 252 | 48% helix, 15% strand | O76290 |
| D | Pteridine reductase (EC 1.5.1.33) | protein | 249 | 48% helix, 15% strand | O76290 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- LYA · 2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic acid · ligand · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · chains B
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 | 1189 | 0.84 | 0.85 | 68 | empty |
| 2 | 611 | 0.77 | 0.83 | 47 | NAP, LYA |
| 3 | 672 | 0.77 | 0.82 | 60 | NAP, LYA |
| 4 | 588 | 0.76 | 0.83 | 48 | NAP, LYA |
| 5 | 579 | 0.76 | 0.82 | 46 | NAP, LYA |
Interfaces
6 interfaces between chains.
- A–C · 1916 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1869 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1412 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1396 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 559 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2X9G · High resolution structure of TbPTR1 in complex with Pemetrexed · 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 2X9G · PDBe 2X9G · UniProt O76290
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