Research workbench

Human PI3KDELTA in complex with LASW1579

Analyse Human PI3KDELTA in complex with LASW1579 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5M6U
Type: protein
Length: 1,080 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, P27986
Ligands: 7KA
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 15% 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	916	45% helix, 18% strand	O00329
B	Phosphatidylinositol 3-kinase regulatory subunit alpha	protein	164	89% helix, 0% strand	P27986

Ligands and binding sites

7KA · 4-azanyl-6-[[(1~{S})-1-(4-oxidanylidene-3-phenyl-pyrrolo[2,1-f][1,2,4]triazin-2-yl) ethyl]amino]pyrimidine-5-carbonitrile · ligand · chains A

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1196	0.81	0.82	81	empty
2	218	0.72	0.88	38	empty
3	107	0.71	0.93	31	empty
4	293	0.70	0.84	45	empty
5	317	0.69	0.83	45	empty

Interfaces

1 interface between chains.

A–B · 1726 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

5M6U · Human PI3KDELTA in complex with LASW1579 · 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 5M6U · PDBe 5M6U · UniProt O00329 · UniProt P27986

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