Research workbench
Crystal structure of human pim-1 kinase in complex with a consensuspeptide and fragment like molekule 2-cyclopropyl-4,5- DIMETHYLTHIENO[5,4-D]PYRIMIDINE-6-carboxylic acid
Analyse Crystal structure of human pim-1 kinase in complex with a consensuspeptide and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N4V
- Type
- protein
- Length
- 282 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
- 8MW
- Pockets
- 3 · best druggability 0.63
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 |
| D | Pimtide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- 8MW · 2-cyclopropyl-4,5-dimethyl-thieno[2,3-d]pyrimidine-6-carboxylic acid · ligand · chains A
- GOL · Glycerol · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.63 | 0.81 | 32 | 8MW, GOL |
| 2 | 146 | 0.59 | 0.84 | 24 | empty |
| 3 | 51 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–D · 608 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5N4V · Crystal structure of human Pim-1 kinase in complex with a consensuspeptide 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 5N4V · PDBe 5N4V · UniProt P11309
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