Research workbench
MPI3KD in complex with INH1
Analyse MPI3KD in complex with INH1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NCY
- Type
- protein
- Length
- 827 residues
- Chains
- 1
- 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
- O35904
- Ligands
- 8TK, SO4
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 18% 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 | 827 | 48% helix, 18% strand | O35904 |
Ligands and binding sites
- 8TK · 4-azanyl-6-[[(1~{S})-1-(3-methyl-5-oxidanylidene-6-phenyl-[1,3]thiazolo[3,2-a]pyridin-7-yl) ethyl]amino]pyrimidine-5-carbonitrile · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1151 | 0.82 | 0.83 | 77 | empty |
| 2 | 641 | 0.69 | 0.77 | 70 | empty |
| 3 | 273 | 0.68 | 0.84 | 33 | empty |
| 4 | 260 | 0.63 | 0.81 | 35 | EDO, 8TK |
| 5 | 105 | 0.51 | 0.81 | 27 | empty |
Compared structures
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 O35904
- Elsewhere: RCSB PDB 5NCY · PDBe 5NCY · UniProt O35904
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