Research workbench
Crystal structure of PHGDH in complex with BI-4924
Analyse Crystal structure of PHGDH in complex with BI-4924 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RJ6
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.984
- Source
- Homo sapiens
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- K5K
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · resolution 1.984 · 2 distinct chains · 39% helix, 16% 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 | 204 | 40% helix, 17% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 210 | 38% helix, 16% strand | O43175 |
Ligands and binding sites
- K5K · 2-[4-[(1~{S})-1-[[4,5-bis(chloranyl)-1,6-dimethyl-indol-2-yl]carbonylamino]-2-oxidanyl-ethyl]phenyl]sulfonylethanoic acid · ligand · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.47 | 0.76 | 31 | K5K |
| 2 | 106 | 0.36 | 0.74 | 24 | empty |
| 3 | 74 | 0.32 | 0.75 | 18 | empty |
| 4 | 66 | 0.31 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2573 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
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 6RJ6 · PDBe 6RJ6 · UniProt O43175
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.