Research workbench
Crystal structure of PIM1 kinase in complex with inhibitor (Z)-2-[(1H- indazol-3-YL)METHYLENE]-6-methoxy-7-(piperazin-1-YLMETHYL)BENZOFURAN- 3(2H)-one
Analyse Crystal structure of PIM1 kinase in complex with inhibitor (Z)-2-[(1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UMW
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene SERINE/THREONINE-protein kinase pim-1
- EC
- 2.7.11.1
- UniProt
- P11309
- Ligands
- 596, SO4
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proto-oncogene SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1) | protein | 264 | 40% helix, 23% strand | P11309 |
Ligands and binding sites
- 596 · (2Z)-2-(1H-indazol-3-ylmethylidene)-6-methoxy-7-(piperazin-1-ylmethyl)-1-benzofuran-3(2H)-one · ligand · chains A
- SO4 · Sulfate ion · ion · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.60 | 0.79 | 27 | 596 |
| 2 | 129 | 0.53 | 0.82 | 22 | empty |
Compared structures
- 3UMW · Crystal structure of Pim1 kinase in complex with inhibitor… · 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 3UMW · PDBe 3UMW · UniProt P11309
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