Research workbench

MPI3KD in complex with 5K

Analyse MPI3KD in complex with 5K in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T28
Type: protein
Length: 822 residues
Chains: 1
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: O35904
Ligands: 74Q
Pockets: 9 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 48% helix, 19% 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	822	48% helix, 19% strand	O35904

Ligands and binding sites

74Q · 3-(benzotriazol-1-yl)-5-[1-methyl-5-(1-phenylcyclopropyl)-1,2,4-triazol-3-yl]pyrazin-2-amine · ligand · chains A

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

Pockets

9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.81	0.82	75	empty
2	1131	0.75	0.77	116	empty
3	291	0.68	0.83	36	empty
4	122	0.67	0.89	26	empty
5	321	0.61	0.78	42	74Q

Modifications

Observed in the structure: 1 isopeptide (isopeptide).

Compared structures

5T28 · mPI3Kd IN COMPLEX WITH 5k · the same entry in another collection · chain A against A, TM-score 1.00
O35904 · 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 O35904
Elsewhere: RCSB PDB 5T28 · PDBe 5T28 · UniProt O35904

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