MolNFT v1 · #40565 · protein
Crystal structure of the human PIM2 in complex with a ruthenium organometallic ligand RU1
2IWI · SERINE/THREONINE-protein kinase pim-2: “Crystal structure of the human PIM2 in complex with a ruthenium organometallic ligand RU1”. X-ray diffraction, 1 ligand (HB1), 4 pockets (best druggability 0.74). MolNFT v1 #40565 on…
- PDB
- 2IWI
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pim-2
- EC
- 2.7.11.1
- UniProt
- Q9P1W9
- Ligands
- HB1
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase pim-2 (EC 2.7.11.1) | protein | 244 | 36% helix, 20% strand | Q9P1W9 |
| B | SERINE/THREONINE-protein kinase pim-2 (EC 2.7.11.1) | protein | 249 | 39% helix, 21% strand | Q9P1W9 |
Ligands and binding sites
- HB1 · Ruthenium-pyridocarbazole-1 · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 755 | 0.74 | 0.79 | 79 | HB1 |
| 2 | 59 | 0.72 | 0.98 | 24 | empty |
| 3 | 318 | 0.65 | 0.80 | 35 | HB1 |
| 4 | 58 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2IWI · Crystal structure of the human PIM2 in complex with a ruthenium organometallic ligand RU1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P1W9 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pim-2 (Q9P1W9) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9P1W9
- Elsewhere: RCSB PDB 2IWI · PDBe 2IWI · UniProt Q9P1W9
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