Research workbench
Crystal structure of bmp-2-inducible kinase in complex with an indazole inhibitor
Analyse Crystal structure of bmp-2-inducible kinase in complex with an indazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I3O
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bmp-2-inducible protein kinase
- EC
- 2.7.11.1
- UniProt
- Q9NSY1
- Ligands
- IDV, SO4
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bmp-2-inducible protein kinase (EC 2.7.11.1) | protein | 302 | 36% helix, 22% strand | Q9NSY1 |
Ligands and binding sites
- IDV · N-(6-{3-[(dimethylsulfamoyl)amino]phenyl}-1H-indazol-3-yl)cyclopropanecarboxamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.78 | 0.83 | 56 | IDV |
| 2 | 340 | 0.71 | 0.83 | 47 | IDV |
| 3 | 142 | 0.52 | 0.80 | 21 | empty |
| 4 | 93 | 0.39 | 0.77 | 19 | empty |
| 5 | 88 | 0.39 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 695 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5I3O · Crystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NSY1 · AlphaFold monomer V2.0 prediction for bmp-2-inducible protein kinase (Q9NSY1) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9NSY1
- Elsewhere: RCSB PDB 5I3O · PDBe 5I3O · UniProt Q9NSY1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.