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Crystal structure of phosphatidylinositol 5-phosphate 4-kinase (PI5P4K2C) bound to an allosteric inhibitor
Analyse Crystal structure of phosphatidylinositol 5-phosphate 4-kinase (PI5P4K2C) bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QIE
- Type
- protein
- Length
- 1,191 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma
- EC
- 2.7.1.149
- UniProt
- Q8TBX8
- Ligands
- DVF
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma (EC 2.7.1.149) | protein | 294 | 36% helix, 24% strand | Q8TBX8 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma (EC 2.7.1.149) | protein | 292 | 36% helix, 24% strand | Q8TBX8 |
| C | Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma (EC 2.7.1.149) | protein | 294 | 36% helix, 24% strand | Q8TBX8 |
| D | Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma (EC 2.7.1.149) | protein | 311 | 34% helix, 23% strand | Q8TBX8 |
Ligands and binding sites
- DVF · 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-(pyridin-2-ylmethyl)pyrrolo[3,2-d]pyrimidin-4-amine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.74 | 0.90 | 20 | DVF |
| 2 | 165 | 0.73 | 0.90 | 20 | DVF |
| 3 | 182 | 0.72 | 0.89 | 22 | DVF |
| 4 | 422 | 0.71 | 0.82 | 45 | DVF |
| 5 | 291 | 0.57 | 0.77 | 37 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1127 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1080 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7QIE · Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C) bound to an… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8TBX8 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 5-phosphate 4-kinase type-2… · a predicted model of the same protein · chain B 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 Q8TBX8
- Elsewhere: RCSB PDB 7QIE · PDBe 7QIE · UniProt Q8TBX8
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