Research workbench
Crystal structure of phosphatidylinositol 5-phosphate 4-kinase (PI5P4K2C) bound to an allosteric inhibitor and AMP-pnp
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
- 7QPN
- Type
- protein
- Length
- 630 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 5-phosphate 4-kinase (PI5P4K2C)
- Ligands
- DVF, ANP
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 5-phosphate 4-kinase (PI5P4K2C) | protein | 317 | 33% helix, 23% strand | — |
| B | Phosphatidylinositol 5-phosphate 4-kinase (PI5P4K2C) | protein | 313 | 33% helix, 23% strand | — |
Ligands and binding sites
- DVF · 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-(pyridin-2-ylmethyl)pyrrolo[3,2-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 186 | 0.74 | 0.90 | 21 | DVF |
| 2 | 195 | 0.73 | 0.89 | 21 | DVF |
| 3 | 311 | 0.67 | 0.82 | 40 | empty |
| 4 | 199 | 0.53 | 0.77 | 23 | empty |
| 5 | 290 | 0.52 | 0.74 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 1122 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7QPN · Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C) bound to an… · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 7QPN · PDBe 7QPN
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