MolNFT v1 · #149660 · protein

Human PI3KDELTA in complex with ligand LASW1976

6G6W · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Human PI3KDELTA in complex with ligand LASW1976”. X-ray diffraction, 1 ligand (EO5), 18 pockets (best druggability 0.83). MolNFT v1 #149660 on GenesisL1: 3D structure…

PDB: 6G6W
Type: protein
Length: 1,078 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: EO5
Pockets: 18 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 52% helix, 17% 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	925	45% helix, 19% strand	O00329
B	Phosphatidylinositol 3-kinase regulatory subunit alpha	protein	153	92% helix, 0% strand	P23727

Ligands and binding sites

EO5 · ~{N}-[3-[4-[[(1~{S})-1-(5-methyl-4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl)ethyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-5-yl]-5-oxidanyl-phenyl]methanesulfonamide · ligand · chains A

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

Pockets

18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	955	0.83	0.85	79	empty
2	716	0.77	0.82	72	empty
3	555	0.73	0.81	50	empty
4	455	0.67	0.79	45	empty
5	281	0.65	0.81	45	empty

Interfaces

1 interface between chains.

A–B · 2400 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6G6W · Human PI3KDELTA in complex with ligand LASW1976 · 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 0.96

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 O00329
Every structure of UniProt P23727
Elsewhere: RCSB PDB 6G6W · PDBe 6G6W · UniProt O00329 · UniProt P23727

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