MolNFT v1 · #117075 · protein
P110ALPHA/P85ALPHA with compound 5
5DXH · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “P110ALPHA/P85ALPHA with compound 5”. X-ray diffraction, 1 ligand (5H2), 20 pockets (best druggability 0.85). MolNFT v1 #117075 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DXH
- Type
- protein
- Length
- 2,216 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform…
- EC
- 2.7.1.153, 2.7.11.1
- UniProt
- P42336, P23727
- Ligands
- 5H2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153, 2.7.11.1) | protein | 989 | 41% helix, 19% strand | P42336 |
| B | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 121 | 95% helix, 0% strand | P23727 |
| D | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153, 2.7.11.1) | protein | 981 | 42% helix, 20% strand | P42336 |
| E | Phosphatidylinositol 3-kinase regulatory subunit alpha | protein | 125 | 94% helix, 0% strand | P23727 |
Ligands and binding sites
- 5H2 · methyl {2-[4-(2-chlorophenyl)-4H-1,2,4-triazol-3-yl]-4,5-dihydrothieno[3,2-d][1]benzoxepin-8-yl}carbamate · ligand · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.85 | 0.85 | 107 | empty |
| 2 | 962 | 0.84 | 0.85 | 86 | empty |
| 3 | 1102 | 0.84 | 0.85 | 116 | empty |
| 4 | 511 | 0.77 | 0.84 | 71 | empty |
| 5 | 576 | 0.74 | 0.82 | 67 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2205 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2112 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5DXH · p110alpha/p85alpha with compound 5 · the same entry in another collection · chain E against E, TM-score 1.00
- P42336 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P23727 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase regulatory subunit… · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P42336
- Every structure of UniProt P23727
- Elsewhere: RCSB PDB 5DXH · PDBe 5DXH · UniProt P42336 · UniProt P23727
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