MolNFT v1 · #59654 · protein
Pim-1 kinase domain in complex with 3-aminophenyl-7- azaindole
3C4E · Proto-oncogene SERINE/THREONINE-protein kinase pim-1: “Pim-1 kinase domain in complex with 3-aminophenyl-7- azaindole”. X-ray diffraction, 1 ligand (C4E), 12 pockets (best druggability 0.70). MolNFT v1 #59654 on GenesisL1: 3D…
- PDB
- 3C4E
- Type
- protein
- Length
- 1,091 residues
- Chains
- 4
- 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
- C4E
- Pockets
- 12 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Proto-oncogene SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1) | protein | 273 | 38% helix, 24% strand | P11309 |
| C | Proto-oncogene SERINE/THREONINE-protein kinase pim-1 (EC 2.7.11.1) | protein | 272 | 39% helix, 23% strand | P11309 |
Ligands and binding sites
- C4E · N-phenyl-1H-pyrrolo[2,3-b]pyridin-3-amine · ligand · 4 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.70 | 0.81 | 53 | empty |
| 2 | 321 | 0.69 | 0.83 | 46 | C4E |
| 3 | 199 | 0.68 | 0.86 | 31 | empty |
| 4 | 334 | 0.68 | 0.82 | 46 | C4E |
| 5 | 280 | 0.67 | 0.82 | 28 | C4E |
Interfaces
3 interfaces between chains.
- B–C · 713 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 692 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3C4E · Pim-1 Kinase Domain in Complex with 3-aminophenyl-7-azaindole · 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 3C4E · PDBe 3C4E · UniProt P11309
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