Research workbench

Human PI3KDELTA in complex with compound 6

Analyse Human PI3KDELTA in complex with compound 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OCO
Type: protein
Length: 1,100 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: M5V
Pockets: 15 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 52% 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	930	45% helix, 19% strand	O00329
B	Phosphatidylinositol 3-kinase regulatory subunit alpha	protein	170	88% helix, 0% strand	P23727

Ligands and binding sites

M5V · 4-[(1S,4S)-5-(3-chlorophenyl)-2,5-diazabicyclo[2.2.1]heptan-2-yl]-2-(pyridin-3-yl) pyrimidine-5-carbonitrile · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1111	0.83	0.84	148	empty
2	895	0.83	0.85	80	empty
3	273	0.65	0.82	38	empty
4	318	0.59	0.77	44	M5V
5	140	0.52	0.80	31	empty

Interfaces

1 interface between chains.

A–B · 2323 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

6OCO · Human PI3KDELTA in complex with compound 6 · 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 0.94

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 6OCO · PDBe 6OCO · UniProt O00329 · UniProt P23727

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