MolNFT v1 · #137348 · protein

Crystal structure of PI3K delta in complex with a trifluoro-ethyl- pyrazol-pyrolotriazine inhibitor

5VLR · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Crystal structure of PI3K delta in complex with a trifluoro-ethyl- pyrazol-pyrolotriazine inhibitor”. X-ray diffraction, 1 ligand (9EM), 14 pockets (best druggability…

PDB: 5VLR
Type: protein
Length: 1,096 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: 9EM
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 50% 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	926	44% helix, 19% strand	O00329
B	Phosphatidylinositol 3-kinase regulatory subunit alpha	protein	170	87% helix, 0% strand	P27986

Ligands and binding sites

9EM · 4-acetyl-1-(3-{4-amino-5-[1-(2,2,2-trifluoroethyl)-1H-pyrazol-5-yl]pyrrolo[2,1-f][1,2,4]triazin-7-yl}phenyl)-3,3-dimethylpiperazin-2-one · ligand · chains A

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

Pockets

14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	936	0.82	0.84	128	empty
2	966	0.81	0.83	89	empty
3	254	0.68	0.84	43	empty
4	125	0.68	0.90	40	empty
5	190	0.62	0.82	26	9EM

Interfaces

1 interface between chains.

A–B · 2170 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

5VLR · Crystal structure of PI3K delta in complex with a trifluoro-ethyl-pyrazol-pyrolotriazine… · 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 5VLR · PDBe 5VLR · UniProt O00329 · UniProt P27986

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