MolNFT v1 · #117087 · protein

P110DELTA/P85ALPHA with gdc-0326

5DXU · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “P110DELTA/P85ALPHA with gdc-0326”. X-ray diffraction, 1 ligand (5H5), 15 pockets (best druggability 0.83). MolNFT v1 #117087 on GenesisL1: 3D structure, binding sites and…

PDB: 5DXU
Type: protein
Length: 1,091 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform…
EC: 2.7.1.153
UniProt: O00329, P23727
Ligands: 5H5
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153)	protein	922	45% helix, 19% strand	O00329
B	Phosphatidylinositol 3-kinase regulatory subunit alpha	protein	169	88% helix, 0% strand	P23727

Ligands and binding sites

5H5 · (2S)-2-({2-[1-(propan-2-yl)-1H-1,2,4-triazol-5-yl]-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepin-9-yl}oxy)propanamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1131	0.83	0.84	131	empty
2	1112	0.81	0.83	88	empty
3	299	0.66	0.81	44	empty
4	173	0.63	0.84	25	5H5
5	81	0.50	0.83	22	empty

Interfaces

1 interface between chains.

A–B · 2305 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

5DXU · p110delta/p85alpha with GDC-0326 · the same entry in another collection · chain A against A, TM-score 1.00
O00329 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate 3-kinase… · a predicted model of the same protein · chain A 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 B against A, TM-score 0.95

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 O00329
Every structure of UniProt P23727
Elsewhere: RCSB PDB 5DXU · PDBe 5DXU · UniProt O00329 · UniProt P23727

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