MolNFT v1 · #103451 · protein
The crystal structure of human VPS34 in complex with pik-III
4PH4 · Phosphatidylinositol 3-kinase catalytic subunit type 3: “The crystal structure of human VPS34 in complex with pik-III”. X-ray diffraction, 1 ligand (2UG), 6 pockets (best druggability 0.67). MolNFT v1 #103451 on GenesisL1: 3D…
- PDB
- 4PH4
- Type
- protein
- Length
- 529 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3-kinase catalytic subunit type 3
- EC
- 2.7.1.137
- UniProt
- Q8NEB9
- Ligands
- 2UG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) | protein | 529 | 57% helix, 9% strand | Q8NEB9 |
Ligands and binding sites
- 2UG · 4'-(cyclopropylmethyl)-N~2~-(pyridin-4-yl)-4,5'-bipyrimidine-2,2'-diamine · ligand · chains B
- GOL · Glycerol · additive · chains 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 | 171 | 0.67 | 0.86 | 21 | empty |
| 2 | 256 | 0.59 | 0.79 | 28 | 2UG |
| 3 | 135 | 0.47 | 0.78 | 21 | empty |
| 4 | 110 | 0.38 | 0.75 | 25 | empty |
| 5 | 52 | 0.32 | 0.78 | 16 | empty |
Compared structures
- 4PH4 · The crystal structure of Human VPS34 in complex with PIK-III · the same entry in another collection · chain B against B, TM-score 1.00
- Q8NEB9 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase catalytic subunit… · 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 Q8NEB9
- Elsewhere: RCSB PDB 4PH4 · PDBe 4PH4 · UniProt Q8NEB9
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