Research workbench
Human PIM1 bound to benzothiophene inhibitor 224
Analyse Human PIM1 bound to benzothiophene inhibitor 224 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PDI
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pim-1; Peptide
- EC
- 2.7.11.1
- UniProt
- P11309
- Ligands
- OCJ
- Pockets
- 3 · best druggability 0.70
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 | 274 | 41% helix, 23% strand | P11309 |
| B | Peptide | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- OCJ · 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide · ligand · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · 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 | 390 | 0.70 | 0.82 | 52 | OCJ |
| 2 | 57 | 0.28 | 0.74 | 16 | empty |
| 3 | 50 | 0.26 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 600 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6PDI · Human PIM1 bound to benzothiophene inhibitor 224 · 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 6PDI · PDBe 6PDI · UniProt P11309
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