MolNFT v1 · #162783 · protein
Crystal structure of phgdh in complex with compound 15
6RJ3 · D-3-phosphoglycerate dehydrogenase: “Crystal structure of phgdh in complex with compound 15”. X-ray diffraction, 2 ligands (K58, SO4), 4 pockets (best druggability 0.67). MolNFT v1 #162783 on GenesisL1: 3D structure, binding sites…
- PDB
- 6RJ3
- Type
- protein
- Length
- 599 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
- K58, SO4
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% 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 | 297 | 41% helix, 19% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 302 | 39% helix, 18% strand | O43175 |
Ligands and binding sites
- K58 · 4-[(1~{R})-1-[(2-methyl-5-phenyl-pyrazol-3-yl) carbonylamino]ethyl]benzoic acid · 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 | 533 | 0.67 | 0.78 | 77 | SO4, K58 |
| 2 | 489 | 0.67 | 0.79 | 55 | SO4 |
| 3 | 69 | 0.34 | 0.75 | 17 | K58 |
| 4 | 56 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2654 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 6RJ3 · Crystal structure of PHGDH in complex with compound 15 · 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 0.99
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 6RJ3 · PDBe 6RJ3 · UniProt O43175
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