MolNFT v1 · #127742 · protein
Crystal structure of human pim-1 kinase in complex with a consensuspeptide and [2-oxo-2-(1H-pyrrol-2-YL)ETHYL] 5-bromo-1H- indole-3-carboxylate
5N5L · SERINE/THREONINE-protein kinase pim-1: “Crystal structure of human pim-1 kinase in complex with a consensuspeptide and…”. X-ray diffraction, 1 ligand (8NZ), 2 pockets (best druggability 0.73). MolNFT v1 #127742 on GenesisL1: 3D…
- PDB
- 5N5L
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pim-1; Pimtide
- EC
- 2.7.11.1
- UniProt
- P11309
- Ligands
- 8NZ
- Pockets
- 2 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1) | protein | 272 | 40% helix, 24% strand | P11309 |
| B | Pimtide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- 8NZ · 5-bromanyl-1~{H}-indole-3-carboxylic acid · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.73 | 0.84 | 52 | 8NZ |
| 2 | 53 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5N5L · Crystal structure of human Pim-1 kinase in complex with a consensuspeptide and… · 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 5N5L · PDBe 5N5L · UniProt P11309
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