MolNFT v1 · #170887 · protein
Crystal structure of compound 1 with PIP4K2A
6YM3 · Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha: “Crystal structure of compound 1 with PIP4K2A”. X-ray diffraction, 2 ligands (OYZ, PO4), 7 pockets (best druggability 0.70). MolNFT v1 #170887 on GenesisL1: 3D structure…
- PDB
- 6YM3
- Type
- protein
- Length
- 626 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
- OYZ, PO4
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149) | protein | 319 | 36% helix, 23% strand | P48426 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (EC 2.7.1.149) | protein | 307 | 35% helix, 23% strand | P48426 |
Ligands and binding sites
- OYZ · (2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.70 | 0.80 | 47 | OYZ |
| 2 | 416 | 0.69 | 0.81 | 41 | OYZ |
| 3 | 116 | 0.44 | 0.77 | 20 | empty |
| 4 | 104 | 0.40 | 0.76 | 22 | empty |
| 5 | 94 | 0.38 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1539 Ų buried · 24 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 6YM3 · PDBe 6YM3 · UniProt P48426
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