MolNFT v1 · #184398 · protein
Crystal structure of PIM1 in complex with arc-3126
7OOX · SERINE/THREONINE-protein kinase pim-1: “Crystal structure of PIM1 in complex with arc-3126”. X-ray diffraction, 3 ligands (06E, NH2, PO4), 2 pockets (best druggability 0.73). MolNFT v1 #184398 on GenesisL1: 3D structure, binding…
- PDB
- 7OOX
- Type
- protein
- Length
- 292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase pim-1; Inhibitor arc-3126
- EC
- 2.7.11.1
- UniProt
- P11309
- Ligands
- 06E, NH2, PO4
- Pockets
- 2 · best druggability 0.73
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-1 (EC 2.7.11.1) | protein | 285 | 38% helix, 21% strand | P11309 |
| B | Inhibitor arc-3126 | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- 06E · 6-[(11-bromanyl-6-oxidanylidene-8-thia-3,5,13-triazatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,10, 12-pentaen-4-yl)methylamino]hexanoic acid · ligand · chains A, B
- NH2 · Amino group · ion · chains B
- PO4 · Phosphate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · 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 | 721 | 0.73 | 0.79 | 58 | 06E |
| 2 | 53 | 0.69 | 0.97 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 594 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 d-amino, 1 covalent (D-amino acid, covalent ligand).
Compared structures
- 7OOX · Crystal structure of PIM1 in complex with ARC-3126 · 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 7OOX · PDBe 7OOX · UniProt P11309
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