Research workbench
Discovery of gdc-0980: a potent, selective, and orally available class I phosphatidylinositol 3-kinase (PI3K)/MAMMALIAN target of rapamycin (mtor) kinase inhibitor for the treatment of cancer
Analyse Discovery of gdc-0980: a potent, selective, and orally available class I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TL5
- Type
- protein
- Length
- 845 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform
- EC
- 2.7.1.153
- UniProt
- P48736
- Ligands
- 980
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (EC 2.7.1.153) | protein | 845 | 44% helix, 17% strand | P48736 |
Ligands and binding sites
- 980 · (2S)-1-(4-{[2-(2-aminopyrimidin-5-yl)-7-methyl-4-(morpholin-4-yl)thieno[3,2-d]pyrimidin-6-yl]methyl}piperazin-1-yl)-2-hydroxypropan-1-one · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.82 | 0.83 | 72 | empty |
| 2 | 483 | 0.68 | 0.79 | 47 | 980 |
| 3 | 306 | 0.66 | 0.81 | 33 | empty |
| 4 | 122 | 0.63 | 0.87 | 22 | empty |
| 5 | 325 | 0.61 | 0.78 | 45 | empty |
Compared structures
- 3TL5 · Discovery of GDC-0980: a Potent, Selective, and Orally Available Class I… · the same entry in another collection · chain A against A, TM-score 1.00
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 P48736
- Elsewhere: RCSB PDB 3TL5 · PDBe 3TL5 · UniProt P48736
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