Research workbench
Crystal structure of PIM1 in complex with arc-1415
Analyse Crystal structure of PIM1 in complex with arc-1415 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OOW
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pim-1; Inhibitor arc-1415
- EC
- 2.7.11.1
- UniProt
- P11309
- Ligands
- 6J9, AZ1, MG, NH2
- Pockets
- 1 · best druggability 0.70
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 |
| B | Inhibitor arc-1415 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- 6J9 · 4-(piperazin-1-yl)-7H-pyrrolo[2,3-d]pyrimidine · ligand · chains A
- AZ1 · Azelaic acid · ligand · chains A, B
- MG · Magnesium ion · metal · chains A
- NH2 · Amino group · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
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 | 376 | 0.70 | 0.82 | 49 | 6J9, MG, EDO |
Interfaces
1 interface between chains.
- A–B · 463 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 d-amino, 1 covalent (D-amino acid, covalent ligand).
Compared structures
- 7OOW · Crystal structure of PIM1 in complex with ARC-1415 · 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 7OOW · PDBe 7OOW · UniProt P11309
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