MolNFT v1 · #162761 · protein
Crystal structure of phgdh in complex with compound 9
6RIH · D-3-phosphoglycerate dehydrogenase: “Crystal structure of phgdh in complex with compound 9”. X-ray diffraction, 2 ligands (K4T, SO4), 4 pockets (best druggability 0.71). MolNFT v1 #162761 on GenesisL1: 3D structure, binding sites…
- PDB
- 6RIH
- Type
- protein
- Length
- 598 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
- K4T, SO4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% 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 | 302 | 37% helix, 18% strand | O43175 |
| B | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 296 | 34% helix, 18% strand | O43175 |
Ligands and binding sites
- K4T · ~{N}-cyclopropyl-2-methyl-5-phenyl-pyrazole-3-carboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.71 | 0.79 | 56 | K4T |
| 2 | 531 | 0.67 | 0.78 | 76 | SO4, K4T |
| 3 | 95 | 0.63 | 0.88 | 22 | empty |
| 4 | 103 | 0.36 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2623 Ų buried · 49 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 6RIH · PDBe 6RIH · UniProt O43175
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