MolNFT v1 · #160472 · protein
Crystal structure of human phgdh complexed with compound 1
6PLF · D-3-phosphoglycerate dehydrogenase: “Crystal structure of human phgdh complexed with compound 1”. X-ray diffraction, 1 ligand (ONV), 7 pockets (best druggability 0.70). MolNFT v1 #160472 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PLF
- Type
- protein
- Length
- 597 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
- ONV
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% 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 | 305 | 41% helix, 18% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 292 | 34% helix, 17% strand | O43175 |
Ligands and binding sites
- ONV · 4-{(1S)-1-[(5-chloro-6-{[(5S)-2-oxo-1,3-oxazolidin-5-yl]methoxy}-1H-indole-2-carbonyl)amino]-2-hydroxyethyl}benzoic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.70 | 0.80 | 69 | ONV |
| 2 | 323 | 0.65 | 0.81 | 46 | empty |
| 3 | 221 | 0.64 | 0.83 | 39 | empty |
| 4 | 139 | 0.57 | 0.83 | 24 | empty |
| 5 | 125 | 0.39 | 0.74 | 32 | EDO |
Interfaces
1 interface between chains.
- A–B · 2547 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6PLF · Crystal structure of human PHGDH complexed with Compound 1 · 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 A 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 6PLF · PDBe 6PLF · UniProt O43175
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