Research workbench
Crystal structure of phgdh in complex with compound 39
Analyse Crystal structure of phgdh in complex with compound 39 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RJ5
- Type
- protein
- Length
- 603 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- K5N, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 301 | 40% helix, 18% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 302 | 41% helix, 18% strand | O43175 |
Ligands and binding sites
- K5N · 2-methyl-~{N}-[(1~{R})-1-[4-(methylsulfonylcarbamoyl) phenyl]ethyl]-5-phenyl-pyrazole-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.67 | 0.78 | 58 | SO4, K5N |
| 2 | 431 | 0.65 | 0.79 | 55 | SO4, K5N |
| 3 | 100 | 0.36 | 0.75 | 18 | empty |
| 4 | 79 | 0.33 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2585 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6RJ5 · Crystal structure of PHGDH in complex with compound 39 · the same entry in another collection · chain A against A, TM-score 1.00
- O43175 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (O43175) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 O43175
- Elsewhere: RCSB PDB 6RJ5 · PDBe 6RJ5 · UniProt O43175
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