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Crystal structure of human pim-1 kinase in complex with a consensus peptide and fragment like molecule 2,5-dihydro-1H-ISOTHIOCHROMENO[3, 4-D]PYRAZOL-3-one
Analyse Crystal structure of human pim-1 kinase in complex with a consensus peptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N4Y
- 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
- 8N5
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 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 | 273 | 39% helix, 23% strand | P11309 |
| B | Pimtide | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- 8N5 · 2,5-dihydro-1~{H}-isothiochromeno[4,3-c]pyrazol-3-one · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.72 | 0.82 | 52 | 8N5 |
| 2 | 62 | 0.28 | 0.73 | 16 | empty |
| 3 | 55 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5N4Y · Crystal structure of human Pim-1 kinase in complex with a consensus peptide and fragment… · 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 5N4Y · PDBe 5N4Y · UniProt P11309
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