MolNFT v1 · #127726 · protein
Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl) acetamide
5N53 · D-3-phosphoglycerate dehydrogenase: “Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with N-(3-chloro-4-methoxyphenyl)…”. X-ray diffraction, 1 ligand (8NB), 4 pockets (best druggability 0.43). MolNFT v1…
- PDB
- 5N53
- Type
- protein
- Length
- 390 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
- UniProt
- O43175
- Ligands
- 8NB
- Pockets
- 4 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) | protein | 195 | 38% helix, 17% strand | O43175 |
Ligands and binding sites
- 8NB · ~{N}-(3-chloranyl-4-methoxy-phenyl)ethanamide · ligand · 2 copies · chains B, A
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 | 141 | 0.43 | 0.76 | 36 | 8NB |
| 2 | 125 | 0.42 | 0.76 | 30 | 8NB |
| 3 | 126 | 0.39 | 0.74 | 28 | empty |
| 4 | 56 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 2546 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 5N53 · Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with… · the same entry in another collection · chain B against B, 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 5N53 · PDBe 5N53 · UniProt O43175
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