Research workbench
PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl- PYRAZOLO[1,5-A]PYRIMIDIN-6-YL]PROPANOIC acid)
Analyse PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NP8
- Type
- protein
- Length
- 404 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase 1
- EC
- 2.7.2.3
- UniProt
- P00558
- Ligands
- 93T, 3PG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 404 | 40% helix, 19% strand | P00558 |
Ligands and binding sites
- 93T · 3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidin-6-yl]propanoic acid · ligand · chains A
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 261 | 0.48 | 0.73 | 40 | EDO |
| 2 | 81 | 0.47 | 0.82 | 24 | empty |
| 3 | 136 | 0.42 | 0.75 | 24 | empty |
Compared structures
- 5NP8 · PGK1 in complex with CRT0063465 (3-[2-(4-bromophenyl)-5,7-dimethyl-pyrazolo[1,5-a]pyrimidi… · the same entry in another collection · chain A against A, TM-score 1.00
- P00558 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 1 (P00558) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00558
- Elsewhere: RCSB PDB 5NP8 · PDBe 5NP8 · UniProt P00558
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