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Crystal structure of human PHGDH complexed with Compound 15
Analyse Crystal structure of human PHGDH complexed with Compound 15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PLG
- Type
- protein
- Length
- 2,418 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.93
- Source
- Homo sapiens
- Molecule
- D-3-phosphoglycerate dehydrogenase
- EC
- 1.1.1.95, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- ONS, MLT
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.93 · 4 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, H | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 303 | 36% helix, 17% strand | O43175 |
| E | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 302 | 37% helix, 17% strand | O43175 |
| F | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 299 | 37% helix, 16% strand | O43175 |
| G | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 302 | 37% helix, 17% strand | O43175 |
Ligands and binding sites
- ONS · (2S)-(4-{3-[(4,5-dichloro-1-methyl-1H-indole-2-carbonyl)amino]oxetan-3-yl}phenyl)(pyridin-3-yl)acetic acid · ligand · 8 copies · chains A, B, D, C, E, F, G, H
- MLT · D-malate · ligand · 4 copies · chains A, E, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.85 | 0.86 | 112 | ONS |
| 2 | 965 | 0.80 | 0.82 | 73 | ONS |
| 3 | 188 | 0.71 | 0.89 | 34 | MLT |
| 4 | 250 | 0.71 | 0.86 | 46 | MLT |
| 5 | 473 | 0.69 | 0.80 | 57 | empty |
Interfaces
8 interfaces between chains.
- D–H · 2545 Ų buried · 41 hydrogen bonds · protein-protein
- C–G · 2544 Ų buried · 39 hydrogen bonds · protein-protein
- A–E · 2502 Ų buried · 25 hydrogen bonds · protein-protein
- B–F · 2492 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 964 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6PLG · Crystal structure of human phgdh complexed with compound 15 · the same entry in another collection · chain H against H, TM-score 1.00
- O43175 · AlphaFold monomer V2.0 prediction for D-3-phosphoglycerate dehydrogenase (O43175) · a predicted model of the same protein · chain E 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 6PLG · PDBe 6PLG · UniProt O43175
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