MolNFT v1 · #127743 · protein
Crystal structure of human pim-1 kinase in complex with a consensuspeptide and (R)-3-(2-((isoquinolin-5-YLMETHYL)(METHYL) CARBAMOYL)PHENYL)PYRROLIDIN-1-ium
5N5M · SERINE/THREONINE-protein kinase pim-1: “Crystal structure of human pim-1 kinase in complex with a consensuspeptide and…”. X-ray diffraction, 1 ligand (8O8), 1 pocket (best druggability 0.71). MolNFT v1 #127743 on GenesisL1: 3D…
- PDB
- 5N5M
- 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
- 8O8
- Pockets
- 1 · best druggability 0.71
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 | 273 | 40% helix, 23% strand | P11309 |
| B | Pimtide | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- 8O8 · ~{N}-(isoquinolin-5-ylmethyl)-~{N}-methyl-2-[(3~{R})-pyrrolidin-3-yl]benzamide · ligand · chains A, B
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 | 438 | 0.71 | 0.81 | 55 | 8O8 |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5N5M · 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 5N5M · PDBe 5N5M · UniProt P11309
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