MolNFT v1 · #157298 · protein
Murine PI3K delta kinsae domain - cpd 3
6MUM · Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic…: “Murine PI3K delta kinsae domain - cpd 3”. X-ray diffraction, 1 ligand (K47), 20 pockets (best druggability 0.81). MolNFT v1 #157298 on GenesisL1: 3D structure, binding…
- PDB
- 6MUM
- Type
- protein
- Length
- 1,648 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
- Q3UDT3
- Ligands
- K47
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% 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 | 826 | 48% helix, 17% strand | Q3UDT3 |
| B | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) | protein | 822 | 47% helix, 17% strand | Q3UDT3 |
Ligands and binding sites
- K47 · [(3S)-3-{[8-(1-ethyl-5-methyl-1H-pyrazol-4-yl)-9-methyl-9H-purin-6-yl]oxy}pyrrolidin-1-yl](oxan-4-yl) methanone · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.81 | 0.82 | 77 | empty |
| 2 | 1184 | 0.81 | 0.82 | 75 | empty |
| 3 | 869 | 0.72 | 0.77 | 87 | empty |
| 4 | 301 | 0.69 | 0.83 | 39 | empty |
| 5 | 315 | 0.69 | 0.83 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 202 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MUM · Murine PI3K delta kinsae domain - cpd 3 · 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 Q3UDT3
- Elsewhere: RCSB PDB 6MUM · PDBe 6MUM · UniProt Q3UDT3
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