Research workbench

Human PI3KDELTA in complex with compound 28

Analyse Human PI3KDELTA in complex with compound 28 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7LQ1
Type: protein
Length: 1,119 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: 2.7.1.137, 2.7.1.153
UniProt: O00329, P27986
Ligands: YA7, CL
Pockets: 15 · best druggability 0.81

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 2.7.1.137, 2.7.1.153)	protein	950	45% helix, 19% strand	O00329
B	Phosphatidylinositol 3-kinase regulatory subunit alpha	protein	169	88% helix, 0% strand	P27986

Ligands and binding sites

YA7 · N-(5-(6-(2-((2S,6R)-2,6-dimethylmorpholino)pyridin-4-yl)-1-oxoisoindolin-4-yl)-2-methoxypyridin-3-yl) methanesulfonamide · ligand · chains A
CL · Chloride ion · ion · 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, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	885	0.81	0.83	104	empty
2	1193	0.81	0.82	98	empty
3	235	0.68	0.85	41	empty
4	281	0.64	0.81	49	empty
5	230	0.62	0.81	31	YA7

Interfaces

1 interface between chains.

A–B · 2358 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7LQ1 · Human PI3KDELTA in complex with compound 28 · 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

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 P27986
Elsewhere: RCSB PDB 7LQ1 · PDBe 7LQ1 · UniProt O00329 · UniProt P27986

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