UniProt Q8NEB9
Phosphatidylinositol 3-kinase catalytic subunit type 3 (Q8NEB9)
Phosphatidylinositol 3-kinase catalytic subunit type 3 (UniProt Q8NEB9), EC 2.7.1.137: 39 experimental structures and 1 predicted model on GenesisL1, 12 ligands bound, 104 pockets. Binding sites, druggability and experiment…
- UniProt
- Q8NEB9
- Protein
- Phosphatidylinositol 3-kinase catalytic subunit type 3
- EC
- 2.7.1.137
- Experimental structures
- 39
- Predicted models
- 1
- Ligands
- 12
- Pockets
- 104 · 13 records with a druggable one
Structures
40 records of Q8NEB9 in the MolNFT archive: 39 experimental, 1 predicted.
| Entry | Title | Method | Chains | Ligands | Pockets |
|---|---|---|---|---|---|
| 3IHY | Human PIK3C3 crystal structure | x-ray diffraction | A, B, C, D, E | — | — |
| 3IHY | Human PIK3C3 crystal structure | x-ray diffraction | A, B, C, D, E | — | — |
| 3LS8 | Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-p… | x-ray diffraction | A, B | — | — |
| 3LS8 | Crystal structure of human PIK3C3 in complex with 3-[4-(4… | x-ray diffraction | A, B | — | — |
| 4OYS | Crystal structure of VPS34 in complex with SAR405. | x-ray diffraction | A | — | — |
| 4OYS | Crystal structure of VPS34 in complex with SAR405. | x-ray diffraction | A | — | — |
| 4PH4 | The crystal structure of Human VPS34 in complex with PIK-III | x-ray diffraction | B | — | — |
| 4PH4 | The crystal structure of human VPS34 in complex with pik-III | x-ray diffraction | B | — | — |
| 4UWF | Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 4UWF | Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 4UWG | Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 4UWG | Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3… | x-ray diffraction | A | — | — |
| 4UWH | Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 4UWH | Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3… | x-ray diffraction | A | — | — |
| 4UWK | Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 4UWK | Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3… | x-ray diffraction | A | — | — |
| 4UWL | Discovery of (2S)-8-((3R)-3-Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 4UWL | Discovery of (2S)-8-((3R)-3-methylmorpholin-4-yl)-1-(3… | x-ray diffraction | A | — | — |
| 5ANL | Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- Methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | RBQ | 6 (best 0.64) |
| 5ANL | Crystal structure of VPS34 in complex with (2S)-8-((3R)-3- methylmorpholin-4-yl)-1-(3-methyl-2-oxo… | x-ray diffraction | A | — | — |
| 5ENN | The crystal structure of Human VPS34 in complex with a selective and potent inhibitor | x-ray diffraction | A, B | 5QS, NA, SO4 | 13 (best 0.67) |
| 5ENN | The crystal structure of human VPS34 in complex with a selective and potent inhibitor | x-ray diffraction | A, B | — | — |
| 6HOG | Structure of VPS34 lir motif bound to gabarap | x-ray diffraction | A | SO4 | — |
| 6HOH | Structure of VPS34 LIR motif (S249E) bound to GABARAP | x-ray diffraction | A, B, C, D | — | — |
| 6HOH | Structure of VPS34 lir motif (S249E) bound to gabarap | x-ray diffraction | A, B, C, D | — | — |
| 6I3U | Optimization of potent and selective ATM inhibitors suitable for a proof-of-concept study in… | x-ray diffraction | A | H2E | 4 (best 0.60) |
| 6I3U | Optimization of potent and selective atm inhibitors suitable for a proof-of-concept study in… | x-ray diffraction | A | H2E | — |
| 6YKG | Structure-based exploration of selectivity for ATM inhibitors in Huntingtons disease | x-ray diffraction | AAA | OZ8 | 3 (best 0.58) |
| 7BL1 | human complex II-BATS bound to membrane-attached Rab5a-GTP | electron microscopy | BBB | — | 8 (best 0.79) |
| 7RSJ | Structure of the VPS34 kinase domain with compound 14 | x-ray diffraction | A | NA, 7IH | 5 (best 0.62) |
| 7RSJ | Structure of the VPS34 kinase domain with compound 14 | x-ray diffraction | A | NA, 7IH | — |
| 7RSP | Structure of the VPS34 kinase domain with compound 14 | x-ray diffraction | A, B | 7IK | 9 (best 0.70) |
| 7RSP | Structure of the VPS34 kinase domain with compound 14 | x-ray diffraction | A, B | 7IK | — |
| 7RSV | Structure of the VPS34 kinase domain with compound 5 | x-ray diffraction | A, B | 7IQ, NA | 12 (best 0.66) |
| 7RSV | Structure of the VPS34 kinase domain with compound 5 | x-ray diffraction | A, B | 7IQ, NA | — |
| 8RXR | Crystal structure of VPS34 in complex with inhibitor SB02024 | x-ray diffraction | A, B | A1H4E | 12 (best 0.64) |
| 8SOR | Structure of human PI3KC3-C1 complex | electron microscopy | B | — | 11 (best 0.70) |
| 9C82 | Structure of human ULK1C:PI3KC3-C1 supercomplex | electron microscopy | B | — | 2 (best 0.83) |
| 9E4V | The structure of human vacuolar protein sorting 34 catalytic domain bound to MES | x-ray diffraction | B | CL, K | 6 (best 0.59) |
| Q8NEB9 | AlphaFold monomer V2.0 prediction for phosphatidylinositol 3-kinase catalytic subunit type 3… | predicted | A | — | 13 (best 0.68) |
Ligands
- NA · Sodium ion · in 5 records
- 7IH · N-{4-[(7R,8R)-4-oxo-7-(propan-2-yl)-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrazin-2-yl]pyridin-2-yl}cyclopropanecarboxamide · in 2 records
- 7IK · (7R,8R)-2-[(3R)-3-methylmorpholin-4-yl]-7-(propan-2-yl)-6,7-dihydropyrazolo[1,5-a]pyrazin-4(5H)-one · in 2 records
- 7IQ · (5as,8ar,9s)-2-[(3R)-3-methylmorpholin-4-yl]-5,5A,6,7, 8,8A-hexahydro-4H-cyclopenta[e]pyrazolo[1,5-a]pyrazin-4-one · in 2 records
- H2E · 2-morpholin-4-yl-6-[7-[(2~{R})-1-morpholin-4-ylpropan-2-yl]oxy-9~{H}-thioxanthen-4-yl]pyran-4-one · in 2 records
- SO4 · Sulfate ion · in 2 records
- 5QS · 1-[[4-(cyclopropylmethyl)-5-[2-(pyridin-4-ylamino)pyrimidin-4-yl]pyrimidin-2-yl]amino]-2-methyl-propan-2-ol · in 1 record
- A1H4E · 4-[(3R)-3-methylmorpholin-4-yl]-2-[(2R)-2-(trifluoromethyl)piperidin-1-yl]-3H-pyridin-6-one · in 1 record
- CL · Chloride ion · in 1 record
- K · Potassium ion · in 1 record
- OZ8 · 4-morpholin-4-yl-6-[(2~{R})-2-(phenylmethyl)pyrrolidin-1-yl]-1~{H}-pyridin-2-one · in 1 record
- RBQ · (8S)-2-(morpholin-4-yl)-9-[2-(propan-2-yloxy)ethyl]-8-(trifluoromethyl)-6,7,8,9-tetrahydro-4H-pyrimido[1,2-a]pyrimidin-4-one · in 1 record
Experiment against prediction
- 3IHY chain B against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.85 Å
- 3IHY chain B against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.85 Å
- 7RSP chain A against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.88 Å
- 7RSP chain A against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.88 Å
- 7RSV chain A against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.89 Å
- 7RSV chain A against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.89 Å
- 3IHY chain D against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.88 Å
- 3IHY chain D against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.88 Å
- 8RXR chain B against the predicted model Q8NEB9: TM-score 0.99, RMSD 1.01 Å
- 7RSV chain B against the predicted model Q8NEB9: TM-score 0.99, RMSD 0.96 Å
Elsewhere
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