MolNFT v1 · #129293 · protein
Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-chloro-4-fluorobenzamide
5OFW · D-3-phosphoglycerate dehydrogenase: “Crystal structure of human 3-phosphoglycerate dehydrogenase in complex with 3-chloro-4-fluorobenzamide”. X-ray diffraction, 1 ligand (9TW), 5 pockets (best druggability 0.46). MolNFT v1 #129293…
- PDB
- 5OFW
- 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, 1.1.1.399, 1.1.1.37
- UniProt
- O43175
- Ligands
- 9TW
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95, 1.1.1.399, 1.1.1.37) | protein | 195 | 40% helix, 17% strand | O43175 |
Ligands and binding sites
- 9TW · 3-chloranyl-4-fluoranyl-benzamide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.46 | 0.75 | 31 | 9TW |
| 2 | 116 | 0.40 | 0.75 | 27 | empty |
| 3 | 93 | 0.37 | 0.76 | 23 | empty |
| 4 | 65 | 0.32 | 0.75 | 16 | 9TW |
| 5 | 62 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- B–A · 2513 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 5OFW · 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 1.00
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 5OFW · PDBe 5OFW · UniProt O43175
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