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Crystal structure of bay-091 with PIP4K2A
Analyse Crystal structure of bay-091 with PIP4K2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YM5
- Type
- protein
- Length
- 618 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
- EC
- 2.7.1.149
- UniProt
- P48426
- Ligands
- OZ5, PO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149) | protein | 312 | 36% helix, 24% strand | P48426 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149) | protein | 306 | 34% helix, 24% strand | P48426 |
Ligands and binding sites
- OZ5 · (2~{R})-2-[[3-cyano-2-[4-(2-fluoranyl-3-methyl-phenyl) phenyl]-1,7-naphthyridin-4-yl]amino]butanoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.69 | 0.80 | 47 | OZ5 |
| 2 | 442 | 0.68 | 0.79 | 44 | OZ5 |
| 3 | 97 | 0.40 | 0.77 | 21 | empty |
| 4 | 87 | 0.38 | 0.77 | 19 | empty |
| 5 | 85 | 0.38 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1525 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
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 P48426
- Elsewhere: RCSB PDB 6YM5 · PDBe 6YM5 · UniProt P48426
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