Research workbench
Discovery of the highly potent PI3K/MTOR dual inhibitor pf-04691502 through structure based drug design
Analyse Discovery of the highly potent PI3K/MTOR dual inhibitor pf-04691502 through… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ML8
- Type
- protein
- Length
- 843 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
- ML8
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 15% 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 | 843 | 43% helix, 15% strand | P48736 |
Ligands and binding sites
- ML8 · 8-cyclopentyl-6-[3-(hydroxymethyl)phenyl]-4-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1144 | 0.82 | 0.83 | 75 | empty |
| 2 | 539 | 0.72 | 0.81 | 55 | ML8 |
| 3 | 357 | 0.64 | 0.79 | 29 | empty |
| 4 | 219 | 0.58 | 0.80 | 31 | empty |
| 5 | 114 | 0.57 | 0.84 | 23 | empty |
Compared structures
- 3ML8 · Discovery of the Highly Potent PI3K/mTOR Dual Inhibitor PF-04691502 through Structure… · 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 3ML8 · PDBe 3ML8 · UniProt P48736
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