Research workbench
Crystal structure of PIM1 kinase in complex with small-molecule inhibitor
Analyse Crystal structure of PIM1 kinase in complex with small-molecule inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O11
- Type
- protein
- Length
- 270 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Homo sapiens
- Molecule
- Serine/threonine-protein kinase pim-1
- EC
- 2.7.11.1
- UniProt
- P11309
- Ligands
- 3NG, CL
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine/threonine-protein kinase pim-1 (EC 2.7.11.1) | protein | 270 | 38% helix, 23% strand | P11309 |
Ligands and binding sites
- 3NG · 5-[(3-chlorophenyl)amino]benzo[c][2,6]naphthyridine-8-carboxylic acid · ligand · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- IMD · Imidazole · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.64 | 0.79 | 41 | 3NG, GOL |
Modifications
Observed in the structure: 2 modified (artifact, phosphorylation).
Compared structures
- 5O11 · Crystal structure of PIM1 kinase in complex with small-molecule inhibitor · 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 P11309
- Elsewhere: RCSB PDB 5O11 · PDBe 5O11 · UniProt P11309
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