MolNFT v1 · #182902 · protein
Crystal structure of PI5P4KIIBETA complex with CC260
7N81 · Phosphatidylinositol 5-phosphate 4-kinase type-2 beta: “Crystal structure of PI5P4KIIBETA complex with CC260”. X-ray diffraction, 1 ligand (HKP), 7 pockets (best druggability 0.74). MolNFT v1 #182902 on GenesisL1: 3D structure…
- PDB
- 7N81
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
- EC
- 2.7.1.149
- UniProt
- P78356
- Ligands
- HKP
- Pockets
- 7 · best druggability 0.74
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 beta (EC 2.7.1.149) | protein | 300 | 35% helix, 23% strand | P78356 |
| B | Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (EC 2.7.1.149) | protein | 307 | 35% helix, 24% strand | P78356 |
Ligands and binding sites
- HKP · (7R)-8-cyclopentyl-7-(cyclopentylmethyl)-2-[(3,5-dichloro-4-hydroxyphenyl)amino]-5-methyl-7,8-dihydropteridin-6(5H)-one · ligand · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.74 | 0.82 | 51 | HKP |
| 2 | 94 | 0.48 | 0.81 | 20 | empty |
| 3 | 97 | 0.44 | 0.79 | 22 | empty |
| 4 | 96 | 0.42 | 0.78 | 21 | empty |
| 5 | 64 | 0.42 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1368 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7N81 · Crystal Structure of PI5P4KIIBeta complex with CC260 · the same entry in another collection · chain A against A, TM-score 1.00
- P78356 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 5-phosphate 4-kinase type-2… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P78356
- Elsewhere: RCSB PDB 7N81 · PDBe 7N81 · UniProt P78356
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