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Human PI3KDELTA in complex with compound 2F

Analyse Human PI3KDELTA in complex with compound 2F in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7JIU
Type: protein
Length: 900 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform
EC: 2.7.1.153, 2.7.11.1
UniProt: P42336
Ligands: VBS
Pockets: 11 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153, 2.7.11.1)	protein	900	45% helix, 17% strand	P42336

Ligands and binding sites

VBS · (3S)-3-benzyl-5-[9-ethyl-8-(2-methylpyrimidin-5-yl)-9H-purin-6-yl]-3-methyl-1,3-dihydro-2H-indol-2-one · ligand · chains A

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

Pockets

11 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	1038	0.85	0.85	88	empty
2	1022	0.77	0.79	97	empty
3	275	0.60	0.79	33	VBS
4	204	0.53	0.77	28	empty
5	161	0.50	0.78	21	empty

Compared structures

7JIU · Human PI3KDELTA in complex with compound 2F · the same entry in another collection · chain A against A, TM-score 1.00
P42336 · 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 0.99

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 P42336
Elsewhere: RCSB PDB 7JIU · PDBe 7JIU · UniProt P42336

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